[PATCH] gnu: Add slurm-llnl.

[PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

* gnu/packages/parallel.scm (slurm-llnl): New variable.
---
 gnu/packages/parallel.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 48 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 8f63bda..03ee460 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -2,7 +2,8 @@
 ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
-;;;
+;;; Copyright © 2014, 2015 Pjotr Prins <pjotr.guix@thebird.nl>
+
 ;;; This file is part of GNU Guix.
 ;;;
 ;;; GNU Guix is free software; you can redistribute it and/or modify it
@@ -20,11 +21,17 @@
 
 (define-module (gnu packages parallel)
   #:use-module (guix packages)
-  #:use-module (guix licenses)
   #:use-module (guix download)
+  #:use-module (guix licenses)
+  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
 
 (define-public parallel
   (package
@@ -47,3 +54,41 @@
 or more computers.  Jobs can consist of single commands or of scripts
 and they are executed on lists of files, hosts, users or other items.")
     (license gpl3+)))
+
+(define-public slurm-llnl
+  (package
+   (name "slurm-llnl")
+   (version "15-08-6-1")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
+                                version ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+             (base32
+              "1h8al21blmrhma9r7qxkba2g5i74m3hrjc9a640j7px54szvg18v"))))
+   (inputs `(("openssl" ,openssl)
+             ("munge" ,munge)
+             ("perl" ,perl)
+             ("expect" ,expect)
+             ("python" ,python)
+             ("linux-pam" , linux-pam)))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags '("--enable-pam")
+      #:phases
+      (modify-phases %standard-phases
+       (add-before
+        'configure 'rewrite-usr-bin
+        (lambda* (#:key inputs #:allow-other-keys)
+                 (substitute* "./doc/html/shtml2html.py"
+                              (("#!/usr/bin/env python")
+                               (string-append "#!" (which "python3"))))
+                 (substitute* "src/common/env.c"
+                              (("/usr/bin/env") (which "env"))))))))
+   (home-page "http://www.schedmd.com/")
+   (synopsis "Tool for cluster computing")
+   (description
+    "Fault-tolerant, and highly scalable cluster management and job
+scheduling system for large and small clusters.")
+   (license license:openssl)))
-- 
2.5.0

Re: [PATCH] gnu: Add slurm-llnl.

[Eric Bavier]

On Wed, 10 Feb 2016 18:36:48 +0100
Pjotr Prins <pjotr.public12@thebird.nl> wrote:

> * gnu/packages/parallel.scm (slurm-llnl): New variable.
> ---
>  gnu/packages/parallel.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++---
>  1 file changed, 48 insertions(+), 3 deletions(-)
> 
> diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
> index 8f63bda..03ee460 100644
> --- a/gnu/packages/parallel.scm
> +++ b/gnu/packages/parallel.scm
> @@ -2,7 +2,8 @@
>  ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
>  ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
>  ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
> -;;;
> +;;; Copyright © 2014, 2015 Pjotr Prins <pjotr.guix@thebird.nl>
> +

Remove this extra whitespace.http://www.schedmd.com/

>  ;;; This file is part of GNU Guix.
>  ;;;
>  ;;; GNU Guix is free software; you can redistribute it and/or modify it
> @@ -20,11 +21,17 @@
>  
>  (define-module (gnu packages parallel)
>    #:use-module (guix packages)
> -  #:use-module (guix licenses)
>    #:use-module (guix download)
> +  #:use-module (guix licenses)
> +  #:use-module ((guix licenses) #:prefix license:)
>    #:use-module (guix build-system gnu)
>    #:use-module (gnu packages)
> -  #:use-module (gnu packages perl))
> +  #:use-module (gnu packages admin)
> +  #:use-module (gnu packages linux)
> +  #:use-module (gnu packages perl)
> +  #:use-module (gnu packages python)
> +  #:use-module (gnu packages tcl)
> +  #:use-module (gnu packages tls))
>  
>  (define-public parallel
>    (package
> @@ -47,3 +54,41 @@
>  or more computers.  Jobs can consist of single commands or of scripts
>  and they are executed on lists of files, hosts, users or other items.")
>      (license gpl3+)))
                ^
With the new 'license:' symbol prefix, all other licenses need to be
adjusted.

> +
> +(define-public slurm-llnl
> +  (package
> +   (name "slurm-llnl")

I think we should rather use "slurm-wlm" if we are trying to
dissambiguate with the "Slurm the Realtime network interface monitor".

> +   (version "15-08-6-1")

Version 15.08.7  is now available.  I would prefer we use '.'s to
separate version number components, and compute the uri string
appropriately.

> +   (source (origin
> +            (method url-fetch)
> +            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
> +                                version ".tar.gz"))
> +            (file-name (string-append name "-" version ".tar.gz"))
> +            (sha256
> +             (base32
> +              "1h8al21blmrhma9r7qxkba2g5i74m3hrjc9a640j7px54szvg18v"))))
> +   (inputs `(("openssl" ,openssl)
> +             ("munge" ,munge)
> +             ("perl" ,perl)
> +             ("expect" ,expect)
> +             ("python" ,python)
> +             ("linux-pam" , linux-pam)))
> +   (build-system gnu-build-system)
> +   (arguments
> +    `(#:configure-flags '("--enable-pam")
> +      #:phases
> +      (modify-phases %standard-phases
> +       (add-before
> +        'configure 'rewrite-usr-bin
> +        (lambda* (#:key inputs #:allow-other-keys)
> +                 (substitute* "./doc/html/shtml2html.py"
> +                              (("#!/usr/bin/env python")
> +                               (string-append "#!" (which "python3"))))

Is this shebang not handled by the patch-shebangs phase?

> +                 (substitute* "src/common/env.c"
> +                              (("/usr/bin/env") (which "env"))))))))
> +   (home-page "http://www.schedmd.com/")

How about "http://slurm.schedmd.com/"?

> +   (synopsis "Tool for cluster computing")

How about "Workload manager" to indicate what the tool does.

> +   (description
> +    "Fault-tolerant, and highly scalable cluster management and job
> +scheduling system for large and small clusters.")
> +   (license license:openssl)))

According to the "License" section at http://www.schedmd.com/#repos
and the COPYING file, it's GPLv2.

`~Eric

Re: [PATCH] gnu: Add slurm-llnl.

[Eric Bavier]

On Wed, 10 Feb 2016 18:36:48 +0100
Pjotr Prins <pjotr.public12@thebird.nl> wrote:

> * gnu/packages/parallel.scm (slurm-llnl): New variable.
> ---
>  gnu/packages/parallel.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++---
>  1 file changed, 48 insertions(+), 3 deletions(-)
[...]
> +   (license license:openssl)))

There are several bits in the 'contribs' directory that seem to not be
under free licenses. E.g.

- contribs/cray/slurmconfgen_smw.py contains "Copyright 2015 Cray Inc.
  All Rights Reserved"

- contribs/cray/slurmconfgen.py.in contains "Copyright 2013 Cray Inc.
  All Rights Reserved"

- contribs/cray/libalps_test_programs.tar.gz contains a mixture of
  GPLv2, public domain, and binaries.

- contribs/mic/mpirun-mic declares no license.

- contribs/pmi2 is under a custom (copyleft?) license.

- contribs/sgather declares no license.

- contribs/sgi/netloc_to_topology.c contains "Copyright (C) 2014
  Silicon Graphics International Corp. All rights reserved."

- contribs/sjobexit/sjobexitmod.pl declares no license.

I don't think we can claim any of these are covered under the same
license as slurm, since the COPYING file explicitely says "Some tools
in the "contribs" directory have other licenses."

The contribs tools are not installed by default, but we do need to
remove any non-free source from there with an origin snippet.

Also, I found the DISCLAIMER file contains the "or (at your option) any
later version." verbiage, so the slurm license itself is license:gpl2+

`~Eric

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

Thanks for the review. This apparently a problematic package. Let's
try fix a few things at a time.

On Wed, Feb 10, 2016 at 10:04:47PM -0600, Eric Bavier wrote:
> >    #:use-module (guix download)
> > +  #:use-module (guix licenses)
> > +  #:use-module ((guix licenses) #:prefix license:)
> >    #:use-module (guix build-system gnu)
> >    #:use-module (gnu packages)

> >  (define-public parallel
> >    (package
> > @@ -47,3 +54,41 @@
> >  or more computers.  Jobs can consist of single commands or of scripts
> >  and they are executed on lists of files, hosts, users or other items.")
> >      (license gpl3+)))
>                 ^
> With the new 'license:' symbol prefix, all other licenses need to be
> adjusted.

I am under the impression one should fix one package at a time. What
is the policy anyway? With or without namespace? Without the namespace
there is a naming conflict between the openssl license and the openssl
package (in tls).

> > +
> > +(define-public slurm-llnl
> > +  (package
> > +   (name "slurm-llnl")
> 
> I think we should rather use "slurm-wlm" if we are trying to
> dissambiguate with the "Slurm the Realtime network interface monitor".

The website https://computing.llnl.gov/linux/slurm/ suggests
otherwise. Also archlinux took this name
https://aur.archlinux.org/packages/slurm-llnl/

> > +   (version "15-08-6-1")
> 
> Version 15.08.7  is now available.  I would prefer we use '.'s to
> separate version number components, and compute the uri string
> appropriately.

OK

> > +   (source (origin
> > +            (method url-fetch)
> > +            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
> > +                                version ".tar.gz"))
> > +            (file-name (string-append name "-" version ".tar.gz"))
> > +            (sha256
> > +             (base32
> > +              "1h8al21blmrhma9r7qxkba2g5i74m3hrjc9a640j7px54szvg18v"))))
> > +   (inputs `(("openssl" ,openssl)
> > +             ("munge" ,munge)
> > +             ("perl" ,perl)
> > +             ("expect" ,expect)
> > +             ("python" ,python)
> > +             ("linux-pam" , linux-pam)))
> > +   (build-system gnu-build-system)
> > +   (arguments
> > +    `(#:configure-flags '("--enable-pam")
> > +      #:phases
> > +      (modify-phases %standard-phases
> > +       (add-before
> > +        'configure 'rewrite-usr-bin
> > +        (lambda* (#:key inputs #:allow-other-keys)
> > +                 (substitute* "./doc/html/shtml2html.py"
> > +                              (("#!/usr/bin/env python")
> > +                               (string-append "#!" (which "python3"))))
> 
> Is this shebang not handled by the patch-shebangs phase?

I added it because the build failed. I'll try again.

> > +                 (substitute* "src/common/env.c"
> > +                              (("/usr/bin/env") (which "env"))))))))
> > +   (home-page "http://www.schedmd.com/")
> 
> How about "http://slurm.schedmd.com/"?

Sure. Arch does different.

> > +   (synopsis "Tool for cluster computing")
> 
> How about "Workload manager" to indicate what the tool does.

Arch has: Simple Linux Utility for Resource Management which is even
less descriptive ;). Besides, slurm runs on more environments.

> > +   (description
> > +    "Fault-tolerant, and highly scalable cluster management and job
> > +scheduling system for large and small clusters.")
> > +   (license license:openssl)))
> 
> According to the "License" section at http://www.schedmd.com/#repos
> and the COPYING file, it's GPLv2.

See next.

-- 

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

On Wed, Feb 10, 2016 at 10:33:30PM -0600, Eric Bavier wrote:
> On Wed, 10 Feb 2016 18:36:48 +0100
> Pjotr Prins <pjotr.public12@thebird.nl> wrote:
> 
> > * gnu/packages/parallel.scm (slurm-llnl): New variable.
> > ---
> >  gnu/packages/parallel.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++---
> >  1 file changed, 48 insertions(+), 3 deletions(-)
> [...]
> > +   (license license:openssl)))
> 
> There are several bits in the 'contribs' directory that seem to not be
> under free licenses. E.g.
> 
> - contribs/cray/slurmconfgen_smw.py contains "Copyright 2015 Cray Inc.
>   All Rights Reserved"
> 
> - contribs/cray/slurmconfgen.py.in contains "Copyright 2013 Cray Inc.
>   All Rights Reserved"
> 
> - contribs/cray/libalps_test_programs.tar.gz contains a mixture of
>   GPLv2, public domain, and binaries.
> 
> - contribs/mic/mpirun-mic declares no license.
> 
> - contribs/pmi2 is under a custom (copyleft?) license.
> 
> - contribs/sgather declares no license.
> 
> - contribs/sgi/netloc_to_topology.c contains "Copyright (C) 2014
>   Silicon Graphics International Corp. All rights reserved."
> 
> - contribs/sjobexit/sjobexitmod.pl declares no license.
> 
> I don't think we can claim any of these are covered under the same
> license as slurm, since the COPYING file explicitely says "Some tools
> in the "contribs" directory have other licenses."
> 
> The contribs tools are not installed by default, but we do need to
> remove any non-free source from there with an origin snippet.
> 
> Also, I found the DISCLAIMER file contains the "or (at your option) any
> later version." verbiage, so the slurm license itself is license:gpl2+

That was hard to find. Initially I had gpl2+ but they don't include the
license in the source so I defaulted to the license they include which
is openssl. But ja...

I agree the rest is a mess but we aren't building contrib. Do you have
an example of a package that does this the right way?

Pj.
-- 

Re: [PATCH] gnu: Add slurm-llnl.

[Ricardo Wurmus]

Pjotr Prins <pjotr.public12@thebird.nl> writes:

> On Wed, Feb 10, 2016 at 10:33:30PM -0600, Eric Bavier wrote:
>> On Wed, 10 Feb 2016 18:36:48 +0100
>> Pjotr Prins <pjotr.public12@thebird.nl> wrote:
>> 
>> > * gnu/packages/parallel.scm (slurm-llnl): New variable.
>> > ---
>> >  gnu/packages/parallel.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++---
>> >  1 file changed, 48 insertions(+), 3 deletions(-)
>> [...]
>> > +   (license license:openssl)))
>> 
>> There are several bits in the 'contribs' directory that seem to not be
>> under free licenses. E.g.
>> 
>> - contribs/cray/slurmconfgen_smw.py contains "Copyright 2015 Cray Inc.
>>   All Rights Reserved"
>> 
>> - contribs/cray/slurmconfgen.py.in contains "Copyright 2013 Cray Inc.
>>   All Rights Reserved"
>> 
>> - contribs/cray/libalps_test_programs.tar.gz contains a mixture of
>>   GPLv2, public domain, and binaries.
>> 
>> - contribs/mic/mpirun-mic declares no license.
>> 
>> - contribs/pmi2 is under a custom (copyleft?) license.
>> 
>> - contribs/sgather declares no license.
>> 
>> - contribs/sgi/netloc_to_topology.c contains "Copyright (C) 2014
>>   Silicon Graphics International Corp. All rights reserved."
>> 
>> - contribs/sjobexit/sjobexitmod.pl declares no license.
>> 
>> I don't think we can claim any of these are covered under the same
>> license as slurm, since the COPYING file explicitely says "Some tools
>> in the "contribs" directory have other licenses."
>> 
>> The contribs tools are not installed by default, but we do need to
>> remove any non-free source from there with an origin snippet.
>> 
>> Also, I found the DISCLAIMER file contains the "or (at your option) any
>> later version." verbiage, so the slurm license itself is license:gpl2+
>
> That was hard to find. Initially I had gpl2+ but they don't include the
> license in the source so I defaulted to the license they include which
> is openssl. But ja...
>
> I agree the rest is a mess but we aren't building contrib. Do you have
> an example of a package that does this the right way?

The best way is to remove the contrib directory in an origin snippet.
We’re doing the same in the “shogun” package (in machine-learning.scm)
as the upstream sources contain files that are not free software.  The
snippet in “shogun” is probably more complicated than what you’ll need
for slurm-llnl; in many cases it’s enough to just do

    (begin
      (delete-file-recursively "contrib")
      #t)

in a snippet.

~~ Ricardo

Re: [PATCH] gnu: Add slurm-llnl.

[Andreas Enge]

On Thu, Feb 11, 2016 at 09:15:34AM +0100, Pjotr Prins wrote:
> I am under the impression one should fix one package at a time. What
> is the policy anyway? With or without namespace? Without the namespace
> there is a naming conflict between the openssl license and the openssl
> package (in tls).

We normally use the namespace as soon as there is a collision; and then I
think it is okay to treat the complete file at once. If you want to be
overcorrect, you could first make the namespace change in one commit and
then add your package in a second one.

> > I think we should rather use "slurm-wlm" if we are trying to
> > dissambiguate with the "Slurm the Realtime network interface monitor".
> The website https://computing.llnl.gov/linux/slurm/ suggests
> otherwise. Also archlinux took this name
> https://aur.archlinux.org/packages/slurm-llnl/

And Debian, but we are free to use our own conventions. Do you think it
is likely that we will package the other slurm? Otherwise, I would simply
go with "slurm" now according to our package guidelines; and then we can
still name the other slurm as slurm-nlm or similar.

Andreas

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

On Thu, Feb 11, 2016 at 11:08:01AM +0100, Andreas Enge wrote:
> > > I think we should rather use "slurm-wlm" if we are trying to
> > > dissambiguate with the "Slurm the Realtime network interface monitor".
> > The website https://computing.llnl.gov/linux/slurm/ suggests
> > otherwise. Also archlinux took this name
> > https://aur.archlinux.org/packages/slurm-llnl/
> 
> And Debian, but we are free to use our own conventions. Do you think it
> is likely that we will package the other slurm? Otherwise, I would simply
> go with "slurm" now according to our package guidelines; and then we can
> still name the other slurm as slurm-nlm or similar.

There is already a slurm package. But it does something different. I
propose we do it my way, so outsiders understand it. Let them flock
over from Debian ;)

Pj.

Re: [PATCH] gnu: Add slurm-llnl.

[Andreas Enge]

On Thu, Feb 11, 2016 at 12:11:27PM +0100, Pjotr Prins wrote:
> There is already a slurm package.

Apparently not in current master:
 $ guix package -A slurm
does not show anything, not even
 $ grep slurm gnu/packages/*.scm

Did I overlook anything?

Andreas

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

On Thu, Feb 11, 2016 at 03:21:21PM +0100, Andreas Enge wrote:
> On Thu, Feb 11, 2016 at 12:11:27PM +0100, Pjotr Prins wrote:
> > There is already a slurm package.
> 
> Did I overlook anything?

No, I also checked.

The point is that https://packages.debian.org/sid/slurm is a network
tool. So, it is about a (potential) name clash. I am happy to call the
cluster manager by its name since it is going in first.

Pj.
-- 

Re: [PATCH] gnu: Add slurm-llnl.

[Eric Bavier]

On Thu, 11 Feb 2016 12:11:27 +0100
Pjotr Prins <pjotr.public12@thebird.nl> wrote:

> On Thu, Feb 11, 2016 at 11:08:01AM +0100, Andreas Enge wrote:
> > > > I think we should rather use "slurm-wlm" if we are trying to
> > > > dissambiguate with the "Slurm the Realtime network interface monitor".
> > > The website https://computing.llnl.gov/linux/slurm/ suggests
> > > otherwise. Also archlinux took this name
> > > https://aur.archlinux.org/packages/slurm-llnl/
> > 
> > And Debian, but we are free to use our own conventions. Do you think it
> > is likely that we will package the other slurm? Otherwise, I would simply
> > go with "slurm" now according to our package guidelines; and then we can
> > still name the other slurm as slurm-nlm or similar.
> 
> There is already a slurm package. But it does something different. I
> propose we do it my way, so outsiders understand it. Let them flock
> over from Debian ;)

In debian, the "slurm-llnl" is a dummy package to help users
transition to the new "slurm-wlm" package.

`~Eric

Re: [PATCH] gnu: Add slurm-llnl.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 3623 bytes --]

On Wed, 10 Feb 2016 18:36:48 +0100
Pjotr Prins <pjotr.public12@thebird.nl> wrote:

> * gnu/packages/parallel.scm (slurm-llnl): New variable.
> ---
>  gnu/packages/parallel.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++---
>  1 file changed, 48 insertions(+), 3 deletions(-)
> 
> diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
> index 8f63bda..03ee460 100644
> --- a/gnu/packages/parallel.scm
> +++ b/gnu/packages/parallel.scm
> @@ -2,7 +2,8 @@
>  ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
>  ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
>  ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
> -;;;
> +;;; Copyright © 2014, 2015 Pjotr Prins <pjotr.guix@thebird.nl>
> +
>  ;;; This file is part of GNU Guix.
>  ;;;
>  ;;; GNU Guix is free software; you can redistribute it and/or modify it
> @@ -20,11 +21,17 @@
>  
>  (define-module (gnu packages parallel)
>    #:use-module (guix packages)
> -  #:use-module (guix licenses)
>    #:use-module (guix download)
> +  #:use-module (guix licenses)
> +  #:use-module ((guix licenses) #:prefix license:)
>    #:use-module (guix build-system gnu)
>    #:use-module (gnu packages)
> -  #:use-module (gnu packages perl))
> +  #:use-module (gnu packages admin)
> +  #:use-module (gnu packages linux)
> +  #:use-module (gnu packages perl)
> +  #:use-module (gnu packages python)
> +  #:use-module (gnu packages tcl)
> +  #:use-module (gnu packages tls))
>  
>  (define-public parallel
>    (package
> @@ -47,3 +54,41 @@
>  or more computers.  Jobs can consist of single commands or of scripts
>  and they are executed on lists of files, hosts, users or other items.")
>      (license gpl3+)))
> +
> +(define-public slurm-llnl
> +  (package
> +   (name "slurm-llnl")
> +   (version "15-08-6-1")
> +   (source (origin
> +            (method url-fetch)
> +            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
> +                                version ".tar.gz"))
> +            (file-name (string-append name "-" version ".tar.gz"))
> +            (sha256
> +             (base32
> +              "1h8al21blmrhma9r7qxkba2g5i74m3hrjc9a640j7px54szvg18v"))))
> +   (inputs `(("openssl" ,openssl)
> +             ("munge" ,munge)
> +             ("perl" ,perl)
> +             ("expect" ,expect)
> +             ("python" ,python)
> +             ("linux-pam" , linux-pam)))
> +   (build-system gnu-build-system)
> +   (arguments
> +    `(#:configure-flags '("--enable-pam")
> +      #:phases
> +      (modify-phases %standard-phases
> +       (add-before
> +        'configure 'rewrite-usr-bin
> +        (lambda* (#:key inputs #:allow-other-keys)
> +                 (substitute* "./doc/html/shtml2html.py"
> +                              (("#!/usr/bin/env python")
> +                               (string-append "#!" (which "python3"))))
> +                 (substitute* "src/common/env.c"
> +                              (("/usr/bin/env") (which "env"))))))))
> +   (home-page "http://www.schedmd.com/")
> +   (synopsis "Tool for cluster computing")
> +   (description
> +    "Fault-tolerant, and highly scalable cluster management and job
                      ^
this comma isn't really needed

> +scheduling system for large and small clusters.")
> +   (license license:openssl)))



-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: OpenPGP digital signature --]
[-- Type: application/pgp-signature, Size: 819 bytes --]

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

On Thu, Feb 11, 2016 at 09:15:34AM +0100, Pjotr Prins wrote:
> > > +   (build-system gnu-build-system)
> > > +   (arguments
> > > +    `(#:configure-flags '("--enable-pam")
> > > +      #:phases
> > > +      (modify-phases %standard-phases
> > > +       (add-before
> > > +        'configure 'rewrite-usr-bin
> > > +        (lambda* (#:key inputs #:allow-other-keys)
> > > +                 (substitute* "./doc/html/shtml2html.py"
> > > +                              (("#!/usr/bin/env python")
> > > +                               (string-append "#!" (which "python3"))))
> > 
> > Is this shebang not handled by the patch-shebangs phase?
> 
> I added it because the build failed. I'll try again.

Now I remember. The python3 package does not have python in the path.

So I patch it with python3.

Pj.

Re: [PATCH] gnu: Add slurm-llnl.

[Andreas Enge]

On Fri, Feb 12, 2016 at 01:20:42PM +0100, Pjotr Prins wrote:
> Now I remember. The python3 package does not have python in the path.
> So I patch it with python3.

Alternatively, I would suggest to use python-wrapper; it is exactly python-3
with symlinks python->python3 etc. added.

Andreas

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

[-- Attachment #1: Type: text/plain, Size: 96 bytes --]

Hopefully taken all comments into account.

For better or for worse, at least this works.

Pj.


[-- Attachment #2: 0001-gnu-Add-slurm-wlm.patch --]
[-- Type: text/x-diff, Size: 5770 bytes --]

From 5941b6b2624ee18444c2fa9f0805136cf6924a88 Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.guix@thebird.nl>
Date: Fri, 12 Feb 2016 13:26:56 +0100
Subject: [PATCH] gnu: Add slurm-wlm.

* gnu/packages/parallel.scm (slurm-wlm): New variable.
---
 gnu/packages/parallel.scm                          | 67 +++++++++++++++++++++-
 ...urm-wlm-configure-remove-nonfree-contribs.patch | 43 ++++++++++++++
 2 files changed, 107 insertions(+), 3 deletions(-)
 create mode 100644 gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 8f63bda..a3e69b3 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,11 +21,18 @@
 
 (define-module (gnu packages parallel)
   #:use-module (guix packages)
-  #:use-module (guix licenses)
   #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system gnu)
+  ;; #:use-module (guix utils)
   #:use-module (gnu packages)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
 
 (define-public parallel
   (package
@@ -46,4 +54,57 @@
      "GNU Parallel is a tool for executing shell jobs in parallel using one
 or more computers.  Jobs can consist of single commands or of scripts
 and they are executed on lists of files, hosts, users or other items.")
-    (license gpl3+)))
+    (license license:gpl3+)))
+
+(define-public slurm-wlm
+  (package
+   (name "slurm-wlm")
+   (version "15.08.7.1")
+   (source (origin
+            (method url-fetch)
+            ;; https://github.com/SchedMD/slurm/archive/slurm-15-08-7-1.tar.gz
+            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
+                                (string-join (string-split version #\.) "-") ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+             (base32
+              "1rmi35l4img00dr4vic8cv8s7b6n1yx1mkq2s7kjf5hvqdh6s2ki"))
+            (patches (list (search-patch "slurm-wlm-configure-remove-nonfree-contribs.patch")))
+            (modules '((guix build utils)))
+            (snippet
+             '(begin
+                (delete-file-recursively "contribs")
+                #t))))
+
+   (inputs `(("openssl" ,openssl)
+             ("munge" ,munge)
+             ("perl" ,perl)
+             ("expect" ,expect)
+             ("python" ,python)
+             ("linux-pam" , linux-pam)))
+   (native-inputs
+    `(("autoconf" ,autoconf)
+      ;; ("automake" ,automake)
+      ))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags '("--enable-pam")
+      #:phases
+      (modify-phases %standard-phases
+       (add-before
+        'configure 'autogen
+        (lambda _ (zero? (system* "autoconf")))) ; configure.ac was patched
+       (add-before
+        'autogen 'rewrite-usr-bin
+        (lambda* (#:key inputs #:allow-other-keys)
+                 (substitute* "./doc/html/shtml2html.py"
+                              (("#!/usr/bin/env python")
+                               (string-append "#!" (which "python3"))))
+                 (substitute* "src/common/env.c"
+                              (("/usr/bin/env") (which "env"))))))))
+   (home-page "http://slurm.schedmd.com/")
+   (synopsis "Workload manager for cluster computing")
+   (description
+    "Fault-tolerant and highly scalable cluster management and job
+scheduling system for large and small clusters.")
+   (license license:gpl2+)))
diff --git a/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
new file mode 100644
index 0000000..b63d5bb
--- /dev/null
+++ b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
@@ -0,0 +1,43 @@
+From 53eda9102b969a4be2882cea4befee03591a7436 Mon Sep 17 00:00:00 2001
+From: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri, 12 Feb 2016 12:43:33 +0100
+Subject: [PATCH] Remove contribs
+
+---
+ configure.ac | 20 --------------------
+ 1 file changed, 20 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index fedf354..e010732 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -438,26 +438,6 @@ dnl All slurm Makefiles:
+ AC_CONFIG_FILES([Makefile
+ 		 config.xml
+ 		 auxdir/Makefile
+-		 contribs/Makefile
+-		 contribs/cray/Makefile
+-		 contribs/cray/csm/Makefile
+-		 contribs/lua/Makefile
+-		 contribs/mic/Makefile
+-		 contribs/pam/Makefile
+-		 contribs/pam_slurm_adopt/Makefile
+-		 contribs/perlapi/Makefile
+-		 contribs/perlapi/libslurm/Makefile
+-		 contribs/perlapi/libslurm/perl/Makefile.PL
+-		 contribs/perlapi/libslurmdb/Makefile
+-		 contribs/perlapi/libslurmdb/perl/Makefile.PL
+-		 contribs/torque/Makefile
+-		 contribs/phpext/Makefile
+-		 contribs/phpext/slurm_php/config.m4
+-		 contribs/sgather/Makefile
+-		 contribs/sgi/Makefile
+-		 contribs/sjobexit/Makefile
+-		 contribs/slurmdb-direct/Makefile
+-		 contribs/pmi2/Makefile
+ 		 doc/Makefile
+ 		 doc/man/Makefile
+ 		 doc/man/man1/Makefile
+-- 
+2.1.4
+
-- 
2.1.4

Re: [PATCH] gnu: Add slurm-llnl.

[Pjotr Prins]

On Fri, Feb 12, 2016 at 01:30:10PM +0100, Andreas Enge wrote:
> On Fri, Feb 12, 2016 at 01:20:42PM +0100, Pjotr Prins wrote:
> > Now I remember. The python3 package does not have python in the path.
> > So I patch it with python3.
> 
> Alternatively, I would suggest to use python-wrapper; it is exactly python-3
> with symlinks python->python3 etc. added.

Well, it is just another dependency. Feel free to adjust if that is
better.

Pj.
-- 

Re: [PATCH] gnu: Add slurm-wlm.

[Pjotr Prins]

[-- Attachment #1: Type: text/plain, Size: 57 bytes --]

Removed a few extraneous comments and changed subject.



[-- Attachment #2: 0001-gnu-Add-slurm-wlm.patch --]
[-- Type: text/x-diff, Size: 5613 bytes --]

From 5941b6b2624ee18444c2fa9f0805136cf6924a88 Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.guix@thebird.nl>
Date: Fri, 12 Feb 2016 13:26:56 +0100
Subject: [PATCH] gnu: Add slurm-wlm.

* gnu/packages/parallel.scm (slurm-wlm): New variable.
---
 gnu/packages/parallel.scm                          | 67 +++++++++++++++++++++-
 ...urm-wlm-configure-remove-nonfree-contribs.patch | 43 ++++++++++++++
 2 files changed, 107 insertions(+), 3 deletions(-)
 create mode 100644 gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 8f63bda..a3e69b3 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,11 +21,18 @@
 
 (define-module (gnu packages parallel)
   #:use-module (guix packages)
-  #:use-module (guix licenses)
   #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
 
 (define-public parallel
   (package
@@ -46,4 +54,57 @@
      "GNU Parallel is a tool for executing shell jobs in parallel using one
 or more computers.  Jobs can consist of single commands or of scripts
 and they are executed on lists of files, hosts, users or other items.")
-    (license gpl3+)))
+    (license license:gpl3+)))
+
+(define-public slurm-wlm
+  (package
+   (name "slurm-wlm")
+   (version "15.08.7.1")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
+                                (string-join (string-split version #\.) "-") ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+             (base32
+              "1rmi35l4img00dr4vic8cv8s7b6n1yx1mkq2s7kjf5hvqdh6s2ki"))
+            (patches (list (search-patch "slurm-wlm-configure-remove-nonfree-contribs.patch")))
+            (modules '((guix build utils)))
+            (snippet
+             '(begin
+                (delete-file-recursively "contribs")
+                #t))))
+
+   (inputs `(("openssl" ,openssl)
+             ("munge" ,munge)
+             ("perl" ,perl)
+             ("expect" ,expect)
+             ("python" ,python)
+             ("linux-pam" , linux-pam)))
+   (native-inputs
+    `(("autoconf" ,autoconf)))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags '("--enable-pam")
+      #:phases
+      (modify-phases %standard-phases
+       (add-before
+        'configure 'autogen
+        (lambda _ (zero? (system* "autoconf")))) ; configure.ac was patched
+       (add-before
+        'autogen 'rewrite-usr-bin
+        (lambda* (#:key inputs #:allow-other-keys)
+                 (substitute* "./doc/html/shtml2html.py"
+                              (("#!/usr/bin/env python")
+                               (string-append "#!" (which "python3"))))
+                 (substitute* "src/common/env.c"
+                              (("/usr/bin/env") (which "env"))))))))
+   (home-page "http://slurm.schedmd.com/")
+   (synopsis "Workload manager for cluster computing")
+   (description
+    "Fault-tolerant and highly scalable cluster management and job
+scheduling system for large and small clusters.")
+   (license license:gpl2+)))
diff --git a/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
new file mode 100644
index 0000000..b63d5bb
--- /dev/null
+++ b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
@@ -0,0 +1,43 @@
+From 53eda9102b969a4be2882cea4befee03591a7436 Mon Sep 17 00:00:00 2001
+From: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri, 12 Feb 2016 12:43:33 +0100
+Subject: [PATCH] Remove contribs
+
+---
+ configure.ac | 20 --------------------
+ 1 file changed, 20 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index fedf354..e010732 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -438,26 +438,6 @@ dnl All slurm Makefiles:
+ AC_CONFIG_FILES([Makefile
+ 		 config.xml
+ 		 auxdir/Makefile
+-		 contribs/Makefile
+-		 contribs/cray/Makefile
+-		 contribs/cray/csm/Makefile
+-		 contribs/lua/Makefile
+-		 contribs/mic/Makefile
+-		 contribs/pam/Makefile
+-		 contribs/pam_slurm_adopt/Makefile
+-		 contribs/perlapi/Makefile
+-		 contribs/perlapi/libslurm/Makefile
+-		 contribs/perlapi/libslurm/perl/Makefile.PL
+-		 contribs/perlapi/libslurmdb/Makefile
+-		 contribs/perlapi/libslurmdb/perl/Makefile.PL
+-		 contribs/torque/Makefile
+-		 contribs/phpext/Makefile
+-		 contribs/phpext/slurm_php/config.m4
+-		 contribs/sgather/Makefile
+-		 contribs/sgi/Makefile
+-		 contribs/sjobexit/Makefile
+-		 contribs/slurmdb-direct/Makefile
+-		 contribs/pmi2/Makefile
+ 		 doc/Makefile
+ 		 doc/man/Makefile
+ 		 doc/man/man1/Makefile
+-- 
+2.1.4
+
-- 
2.1.4

Re: [PATCH] gnu: Add slurm-wlm.

[Andreas Enge]

Hi Piotr,

"git am" fails on current master with this patch, claiming an error at
line 39:
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
etc.

Did we not agree in the end that the package should simply be called slurm?

Could you please send a patch that applies to current master?

Thanks,

Andreas

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

[-- Attachment #1: Type: text/plain, Size: 194 bytes --]

Another package name (this time we go down to slurm), another patch.
I also put the modules in alphabetic order when adding the license
name space. Hope that doesn't need a separate patch.

Pj.

[-- Attachment #2: 0001-gnu-Add-slurm.patch --]
[-- Type: text/x-diff, Size: 5948 bytes --]

From ef998204cde384d35b605509be09b25170c28fb8 Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Sat, 13 Feb 2016 09:45:30 +0100
Subject: [PATCH] gnu: Add slurm.

* gnu/packages/parallel.scm (slurm): New variable.
* gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch: New file.
* gnu/packages/parallel.scm (parallel): Introduce license name space.
---
 gnu/packages/parallel.scm                          | 67 ++++++++++++++++++++--
 ...urm-wlm-configure-remove-nonfree-contribs.patch | 43 ++++++++++++++
 2 files changed, 105 insertions(+), 5 deletions(-)
 create mode 100644 gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 8f63bda..a52e554 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,12 +20,18 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages parallel)
-  #:use-module (guix packages)
-  #:use-module (guix licenses)
-  #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
   #:use-module (gnu packages)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
 
 (define-public parallel
   (package
@@ -46,4 +53,54 @@
      "GNU Parallel is a tool for executing shell jobs in parallel using one
 or more computers.  Jobs can consist of single commands or of scripts
 and they are executed on lists of files, hosts, users or other items.")
-    (license gpl3+)))
+    (license license:gpl3+)))
+
+(define-public slurm
+  (package
+   (name "slurm")
+   (version "15.08.7.1")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
+                                (string-join (string-split version #\.) "-") ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+             (base32
+              "1rmi35l4img00dr4vic8cv8s7b6n1yx1mkq2s7kjf5hvqdh6s2ki"))
+            (patches (list (search-patch "slurm-wlm-configure-remove-nonfree-contribs.patch")))
+            (modules '((guix build utils)))
+            (snippet
+             '(begin
+                (delete-file-recursively "contribs")
+                #t))))
+   (inputs `(("openssl" ,openssl)
+             ("munge" ,munge)
+             ("perl" ,perl)
+             ("expect" ,expect)
+             ("python" ,python)
+             ("linux-pam" , linux-pam)))
+   (native-inputs
+    `(("autoconf" ,autoconf)))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags '("--enable-pam")
+      #:phases
+      (modify-phases %standard-phases
+       (add-before
+        'configure 'autogen
+        (lambda _ (zero? (system* "autoconf")))) ; configure.ac was patched
+       (add-before
+        'autogen 'rewrite-usr-bin
+        (lambda* (#:key inputs #:allow-other-keys)
+                 ;; replace python call with python3
+                 (substitute* "./doc/html/shtml2html.py" 
+                              (("#!/usr/bin/env python")
+                               (string-append "#!" (which "python3"))))
+                 (substitute* "src/common/env.c"
+                              (("/usr/bin/env") (which "env"))))))))
+   (home-page "http://slurm.schedmd.com/")
+   (synopsis "Workload manager for cluster computing")
+   (description
+    "Fault-tolerant and highly scalable cluster management and job
+scheduling system for large and small clusters.")
+   (license license:gpl2+)))
diff --git a/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
new file mode 100644
index 0000000..b63d5bb
--- /dev/null
+++ b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
@@ -0,0 +1,43 @@
+From 53eda9102b969a4be2882cea4befee03591a7436 Mon Sep 17 00:00:00 2001
+From: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri, 12 Feb 2016 12:43:33 +0100
+Subject: [PATCH] Remove contribs
+
+---
+ configure.ac | 20 --------------------
+ 1 file changed, 20 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index fedf354..e010732 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -438,26 +438,6 @@ dnl All slurm Makefiles:
+ AC_CONFIG_FILES([Makefile
+ 		 config.xml
+ 		 auxdir/Makefile
+-		 contribs/Makefile
+-		 contribs/cray/Makefile
+-		 contribs/cray/csm/Makefile
+-		 contribs/lua/Makefile
+-		 contribs/mic/Makefile
+-		 contribs/pam/Makefile
+-		 contribs/pam_slurm_adopt/Makefile
+-		 contribs/perlapi/Makefile
+-		 contribs/perlapi/libslurm/Makefile
+-		 contribs/perlapi/libslurm/perl/Makefile.PL
+-		 contribs/perlapi/libslurmdb/Makefile
+-		 contribs/perlapi/libslurmdb/perl/Makefile.PL
+-		 contribs/torque/Makefile
+-		 contribs/phpext/Makefile
+-		 contribs/phpext/slurm_php/config.m4
+-		 contribs/sgather/Makefile
+-		 contribs/sgi/Makefile
+-		 contribs/sjobexit/Makefile
+-		 contribs/slurmdb-direct/Makefile
+-		 contribs/pmi2/Makefile
+ 		 doc/Makefile
+ 		 doc/man/Makefile
+ 		 doc/man/man1/Makefile
+-- 
+2.1.4
+
-- 
2.1.4

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Sat, Feb 13, 2016 at 09:59:40AM +0100, Pjotr Prins wrote:
> Another package name (this time we go down to slurm), another patch.

Actually, the name of the patch file: slurm-wml-....patch should also
be changed... And it needs to be registered in gnu-system.am.

Some lines are way beyond 80 characters; this should be detected by
"guix lint".

> I also put the modules in alphabetic order when adding the license
> name space. Hope that doesn't need a separate patch.

I think that is fine.

However, your patch still does not apply on top of master:
Applying: gnu: Add slurm.
.git/rebase-apply/patch:87: trailing whitespace.
                 (substitute* "./doc/html/shtml2html.py" 
.git/rebase-apply/patch:119: space before tab in indent.
                 config.xml
.git/rebase-apply/patch:120: space before tab in indent.
                 auxdir/Makefile
.git/rebase-apply/patch:141: space before tab in indent.
                 doc/Makefile
.git/rebase-apply/patch:142: space before tab in indent.
                 doc/man/Makefile
error: patch failed: gnu/packages/parallel.scm:2
error: gnu/packages/parallel.scm: patch does not apply
Patch failed at 0001 gnu: Add slurm.

I do not think that the whitespace is a real issue; did you rebase before
sending the patch? It is quite curious since the parallel.scm file has not
been changed yet this year.

Andreas

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

On Sat, Feb 13, 2016 at 11:28:25AM +0100, Andreas Enge wrote:
> Some lines are way beyond 80 characters; this should be detected by
> "guix lint".

guix lint has not been working for me:

./pre-inst-env guix lint slurm
warning: failed to install locale: Invalid argument
filtered-port: failed to execute ' -dc ': No such file or directory
Backtrace:
In unknown file:
   ?: 19 [apply-smob/1 #<catch-closure 243f940>]
In ice-9/boot-9.scm:
  63: 18 [call-with-prompt prompt0 ...]
In ice-9/eval.scm:
 432: 17 [eval # #]
In ice-9/boot-9.scm:
(...)
In guix/utils.scm:
 255: 5 [call-with-decompressed-port gzip ...]
In guix/cve.scm:
 143: 4 [#<procedure 3552980 at guix/cve.scm:139:3 (port)> #<closed: file 0>]
 133: 3 [xml->vulnerabilities #<closed: file 0>]
In ice-9/boot-9.scm:
 105: 2 [#<procedure 23d1180 at ice-9/boot-9.scm:97:6 (thrown-k . args)> parser-error ...]
  65: 1 [abort-to-prompt catch7 parser-error ...]
In unknown file:
   ?: 0 [scm-error misc-error #f "~A ~S" ("decompressed-port failure" (6495)) #f]

ERROR: In procedure scm-error:
ERROR: decompressed-port failure (6495)

any idea what this could be?

> However, your patch still does not apply on top of master:
> Applying: gnu: Add slurm.
> .git/rebase-apply/patch:87: trailing whitespace.
>                  (substitute* "./doc/html/shtml2html.py" 
> .git/rebase-apply/patch:119: space before tab in indent.
>                  config.xml
> .git/rebase-apply/patch:120: space before tab in indent.
>                  auxdir/Makefile
> .git/rebase-apply/patch:141: space before tab in indent.
>                  doc/Makefile
> .git/rebase-apply/patch:142: space before tab in indent.
>                  doc/man/Makefile
> error: patch failed: gnu/packages/parallel.scm:2
> error: gnu/packages/parallel.scm: patch does not apply
> Patch failed at 0001 gnu: Add slurm.
> 
> I do not think that the whitespace is a real issue; did you rebase before
> sending the patch? It is quite curious since the parallel.scm file has not
> been changed yet this year.

I am using a recent repo of guix. I did do a rebase and the patch applies
on my tree (as did the previous one). Is there no more information?

Pj.

-- 

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Sat, Feb 13, 2016 at 05:42:57PM +0100, Pjotr Prins wrote:
> On Sat, Feb 13, 2016 at 11:28:25AM +0100, Andreas Enge wrote:
> > Some lines are way beyond 80 characters; this should be detected by
> > "guix lint".
> guix lint has not been working for me:

Strange, it works for me with other packages.

> I am using a recent repo of guix. I did do a rebase and the patch applies
> on my tree (as did the previous one). Is there no more information?

No, that is all (except a few more lines explaining what to do now in a git
context). Could these two issues be related?

It would be good if someone else could try to apply the patch.

Andreas

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

On Sat, Feb 13, 2016 at 05:42:57PM +0100, Pjotr Prins wrote:
> > However, your patch still does not apply on top of master:
> I am using a recent repo of guix. I did do a rebase and the patch applies
> on my tree (as did the previous one). Is there no more information?

git pull origin master
From git://git.savannah.gnu.org/guix
 * branch            master     -> FETCH_HEAD
Updating a747bab..a42d99f
Fast-forward
 gnu/packages/ebook.scm | 4 ++--
 gnu/packages/maths.scm | 4 ++--
 gnu/packages/ocaml.scm | 6 ++++++
 3 files changed, 10 insertions(+), 4 deletions(-)
bergamo:~/izip/git/opensource/scheme/guix$ git log
commit a42d99f2843d3880cad2f20777b4bd1f969c38dd
Author: Andreas Enge <andreas@enge.fr>
Date:   Sat Feb 13 14:34:50 2016 +0100

    gnu: calibre: Update to 2.51.0.
    
    * gnu/packages/ebook.scm (calibre): Update to 2.51.0.

(i.e. latest)

cat 0001-gnu-Add-slurm.patch |patch -p1  # same patch, different name
patching file gnu/packages/parallel.scm
patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch

Works fine. Maybe because I used an attachment previously?

I'll send it again after renaming the patch.

-- 

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

OK, patch coming up.

On Sat, Feb 13, 2016 at 11:28:25AM +0100, Andreas Enge wrote:
> On Sat, Feb 13, 2016 at 09:59:40AM +0100, Pjotr Prins wrote:
> > Another package name (this time we go down to slurm), another patch.
> 
> Actually, the name of the patch file: slurm-wml-....patch should also
> be changed... And it needs to be registered in gnu-system.am.
> 
> Some lines are way beyond 80 characters; this should be detected by
> "guix lint".

Only one line that I can tell

  (patches (list (search-patch "slurm-wlm-configure-remove-nonfree-contribs.patch")))

> > I also put the modules in alphabetic order when adding the license
> > name space. Hope that doesn't need a separate patch.
> 
> I think that is fine.
> 
> However, your patch still does not apply on top of master:
> Applying: gnu: Add slurm.
> .git/rebase-apply/patch:87: trailing whitespace.
>                  (substitute* "./doc/html/shtml2html.py" 
> .git/rebase-apply/patch:119: space before tab in indent.
>                  config.xml
> .git/rebase-apply/patch:120: space before tab in indent.
>                  auxdir/Makefile
> .git/rebase-apply/patch:141: space before tab in indent.
>                  doc/Makefile
> .git/rebase-apply/patch:142: space before tab in indent.
>                  doc/man/Makefile
> error: patch failed: gnu/packages/parallel.scm:2
> error: gnu/packages/parallel.scm: patch does not apply
> Patch failed at 0001 gnu: Add slurm.
> 
> I do not think that the whitespace is a real issue; did you rebase before
> sending the patch? It is quite curious since the parallel.scm file has not
> been changed yet this year.

I double checked. There is no tabs or trailing whitespace in the
package.

Anyway try again. If it fails I give up. I have had enough of slurm
and for now of sending patches back and forth.

Pj.

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Sat, Feb 13, 2016 at 06:01:19PM +0100, Pjotr Prins wrote:
> cat 0001-gnu-Add-slurm.patch |patch -p1  # same patch, different name
> patching file gnu/packages/parallel.scm
> patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
> Works fine. Maybe because I used an attachment previously?

No, that should not be a problem (after I removed the first line ">From..."
of the attachment). I still get:

patching file gnu/packages/parallel.scm
Hunk #1 FAILED at 2.
1 out of 3 hunks FAILED -- saving rejects to file gnu/packages/parallel.scm.rej
patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch

The thing that does not work is adding your copyright line. Very strange;
we seem to have the same white-space in the file.

Andreas

Re: [PATCH] gnu: Add slurm.

[Leo Famulari]

On Sat, Feb 13, 2016 at 06:20:01PM +0100, Andreas Enge wrote:
> On Sat, Feb 13, 2016 at 06:01:19PM +0100, Pjotr Prins wrote:
> > cat 0001-gnu-Add-slurm.patch |patch -p1  # same patch, different name
> > patching file gnu/packages/parallel.scm
> > patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
> > Works fine. Maybe because I used an attachment previously?
> 
> No, that should not be a problem (after I removed the first line ">From..."
> of the attachment). I still get:
> 
> patching file gnu/packages/parallel.scm
> Hunk #1 FAILED at 2.
> 1 out of 3 hunks FAILED -- saving rejects to file gnu/packages/parallel.scm.rej
> patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
> 
> The thing that does not work is adding your copyright line. Very strange;
> we seem to have the same white-space in the file.

I had the same issue with some of Jan's patches yesterday.

I used diffoscope to compare the non-working patch and a "should-be"
identical patch that I generated locally. The only differences were in
the patch headers and the encoding of the file (UTF-8 vs ISO-8859-1).

I couldn't figure out why these differences would matter and moved on,
but it's disturbing that others are hitting the same issue!

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Sat, Feb 13, 2016 at 03:13:37PM -0500, Leo Famulari wrote:
> I used diffoscope to compare the non-working patch and a "should-be"
> identical patch that I generated locally. The only differences were in
> the patch headers and the encoding of the file (UTF-8 vs ISO-8859-1).

I think that explains it: The non-working part of the patch was the copyright
line, which contains the copyright symbol!

So let us all move to utf-8!

Andreas

Re: [PATCH] gnu: Add slurm.

[Leo Famulari]

[-- Attachment #1: Type: text/plain, Size: 2383 bytes --]

On Sat, Feb 13, 2016 at 03:13:37PM -0500, Leo Famulari wrote:
> On Sat, Feb 13, 2016 at 06:20:01PM +0100, Andreas Enge wrote:
> > On Sat, Feb 13, 2016 at 06:01:19PM +0100, Pjotr Prins wrote:
> > > cat 0001-gnu-Add-slurm.patch |patch -p1  # same patch, different name
> > > patching file gnu/packages/parallel.scm
> > > patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
> > > Works fine. Maybe because I used an attachment previously?
> > 
> > No, that should not be a problem (after I removed the first line ">From..."
> > of the attachment). I still get:
> > 
> > patching file gnu/packages/parallel.scm
> > Hunk #1 FAILED at 2.
> > 1 out of 3 hunks FAILED -- saving rejects to file gnu/packages/parallel.scm.rej
> > patching file gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
> > 
> > The thing that does not work is adding your copyright line. Very strange;
> > we seem to have the same white-space in the file.
> 
> I had the same issue with some of Jan's patches yesterday.
> 
> I used diffoscope to compare the non-working patch and a "should-be"
> identical patch that I generated locally. The only differences were in
> the patch headers and the encoding of the file (UTF-8 vs ISO-8859-1).
> 
> I couldn't figure out why these differences would matter and moved on,
> but it's disturbing that others are hitting the same issue!

I investigated some more. I used the patch that is upthread of what I am
replying to.

I applied the patch with `patch -p1 < ...`. I could have used `git am`
but I'm not doing it again ;)

Everything applied except for Pjotr's attribution in parallel.scm, so I
manually copied that into the file.

Then, I added all the changes to the index, committed, and used `git
format-patch` to create a patch on master. I'll show you:

$ git add -u
$ git add gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
$ git commit -m "patch-test"
$ git format-patch -n --thread=shallow master
$ git reset --hard HEAD^ # roll back one commit
$ git am 0001-patch-test.patch
$ echo $?
0
$ diffoscope --html report.html 0001-patch-test.patch 0001-gnu-Add-slurm.patch

I've attached report.html and 0001-patch-test.patch for your inspection.

I wonder if the version of git is a factor? 2.1.4 vs 2.6.3. Jan was also
using 2.1.4, and his patches also failed *only* on the attribution line.

[-- Attachment #2: report.html --]
[-- Type: text/html, Size: 30348 bytes --]

[-- Attachment #3: 0001-patch-test.patch --]
[-- Type: text/x-diff, Size: 5666 bytes --]

From 788a22631663d1e4060ebe87b4272c590f138a25 Mon Sep 17 00:00:00 2001
Message-Id: <788a22631663d1e4060ebe87b4272c590f138a25.1455395436.git.leo@famulari.name>
From: Leo Famulari <leo@famulari.name>
Date: Sat, 13 Feb 2016 15:30:30 -0500
Subject: [PATCH 1/1] patch test

---
 gnu/packages/parallel.scm                          | 67 ++++++++++++++++++++--
 ...urm-wlm-configure-remove-nonfree-contribs.patch | 43 ++++++++++++++
 2 files changed, 105 insertions(+), 5 deletions(-)
 create mode 100644 gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 8f63bda..a52e554 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,12 +20,18 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages parallel)
-  #:use-module (guix packages)
-  #:use-module (guix licenses)
-  #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
   #:use-module (gnu packages)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
 
 (define-public parallel
   (package
@@ -46,4 +53,54 @@
      "GNU Parallel is a tool for executing shell jobs in parallel using one
 or more computers.  Jobs can consist of single commands or of scripts
 and they are executed on lists of files, hosts, users or other items.")
-    (license gpl3+)))
+    (license license:gpl3+)))
+
+(define-public slurm
+  (package
+   (name "slurm")
+   (version "15.08.7.1")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
+                                (string-join (string-split version #\.) "-") ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+             (base32
+              "1rmi35l4img00dr4vic8cv8s7b6n1yx1mkq2s7kjf5hvqdh6s2ki"))
+            (patches (list (search-patch "slurm-wlm-configure-remove-nonfree-contribs.patch")))
+            (modules '((guix build utils)))
+            (snippet
+             '(begin
+                (delete-file-recursively "contribs")
+                #t))))
+   (inputs `(("openssl" ,openssl)
+             ("munge" ,munge)
+             ("perl" ,perl)
+             ("expect" ,expect)
+             ("python" ,python)
+             ("linux-pam" , linux-pam)))
+   (native-inputs
+    `(("autoconf" ,autoconf)))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags '("--enable-pam")
+      #:phases
+      (modify-phases %standard-phases
+       (add-before
+        'configure 'autogen
+        (lambda _ (zero? (system* "autoconf")))) ; configure.ac was patched
+       (add-before
+        'autogen 'rewrite-usr-bin
+        (lambda* (#:key inputs #:allow-other-keys)
+                 ;; replace python call with python3
+                 (substitute* "./doc/html/shtml2html.py" 
+                              (("#!/usr/bin/env python")
+                               (string-append "#!" (which "python3"))))
+                 (substitute* "src/common/env.c"
+                              (("/usr/bin/env") (which "env"))))))))
+   (home-page "http://slurm.schedmd.com/")
+   (synopsis "Workload manager for cluster computing")
+   (description
+    "Fault-tolerant and highly scalable cluster management and job
+scheduling system for large and small clusters.")
+   (license license:gpl2+)))
diff --git a/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
new file mode 100644
index 0000000..b63d5bb
--- /dev/null
+++ b/gnu/packages/patches/slurm-wlm-configure-remove-nonfree-contribs.patch
@@ -0,0 +1,43 @@
+From 53eda9102b969a4be2882cea4befee03591a7436 Mon Sep 17 00:00:00 2001
+From: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri, 12 Feb 2016 12:43:33 +0100
+Subject: [PATCH] Remove contribs
+
+---
+ configure.ac | 20 --------------------
+ 1 file changed, 20 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index fedf354..e010732 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -438,26 +438,6 @@ dnl All slurm Makefiles:
+ AC_CONFIG_FILES([Makefile
+ 		 config.xml
+ 		 auxdir/Makefile
+-		 contribs/Makefile
+-		 contribs/cray/Makefile
+-		 contribs/cray/csm/Makefile
+-		 contribs/lua/Makefile
+-		 contribs/mic/Makefile
+-		 contribs/pam/Makefile
+-		 contribs/pam_slurm_adopt/Makefile
+-		 contribs/perlapi/Makefile
+-		 contribs/perlapi/libslurm/Makefile
+-		 contribs/perlapi/libslurm/perl/Makefile.PL
+-		 contribs/perlapi/libslurmdb/Makefile
+-		 contribs/perlapi/libslurmdb/perl/Makefile.PL
+-		 contribs/torque/Makefile
+-		 contribs/phpext/Makefile
+-		 contribs/phpext/slurm_php/config.m4
+-		 contribs/sgather/Makefile
+-		 contribs/sgi/Makefile
+-		 contribs/sjobexit/Makefile
+-		 contribs/slurmdb-direct/Makefile
+-		 contribs/pmi2/Makefile
+ 		 doc/Makefile
+ 		 doc/man/Makefile
+ 		 doc/man/man1/Makefile
+-- 
+2.1.4
+
-- 
2.6.3

Re: [PATCH] gnu: Add slurm.

[Leo Famulari]

On Sat, Feb 13, 2016 at 09:34:22PM +0100, Andreas Enge wrote:
> On Sat, Feb 13, 2016 at 03:13:37PM -0500, Leo Famulari wrote:
> > I used diffoscope to compare the non-working patch and a "should-be"
> > identical patch that I generated locally. The only differences were in
> > the patch headers and the encoding of the file (UTF-8 vs ISO-8859-1).
> 
> I think that explains it: The non-working part of the patch was the copyright
> line, which contains the copyright symbol!
> 
> So let us all move to utf-8!

If that is it, then I believe git should "do the right thing" when
generating patches. I've noticed that it progressively sets the encoding
based on the minimum required to encode the characters in the patch.

For example, if all characters can be encoded in ASCII, it uses ASCII,
otherwise I think it uses UTF-8.

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

On Sat, Feb 13, 2016 at 03:38:46PM -0500, Leo Famulari wrote:
> I wonder if the version of git is a factor? 2.1.4 vs 2.6.3. Jan was also
> using 2.1.4, and his patches also failed *only* on the attribution line.

Thank you Leo and Andreas for restoring my sanity! 

I'll upgrade git. I was using the newer version in my build
environment but generating the patch in an older version. Also locales
I need to settle on. I tend to have en_GB on Debian, but in a guix
shell it may act strange if I don't specify locales.

And I won't add attribution again ;). I.e., the combination of being
an old git, having wrong locales and injecting self-attribution, was
lethal. 

Pj.

Re: [PATCH] gnu: Add slurm.

[Leo Famulari]

On Sat, Feb 13, 2016 at 10:32:01PM +0100, Pjotr Prins wrote:
> On Sat, Feb 13, 2016 at 03:38:46PM -0500, Leo Famulari wrote:
> > I wonder if the version of git is a factor? 2.1.4 vs 2.6.3. Jan was also
> > using 2.1.4, and his patches also failed *only* on the attribution line.
> 
> Thank you Leo and Andreas for restoring my sanity! 
> 
> I'll upgrade git. I was using the newer version in my build
> environment but generating the patch in an older version. Also locales
> I need to settle on. I tend to have en_GB on Debian, but in a guix
> shell it may act strange if I don't specify locales.
> 
> And I won't add attribution again ;). I.e., the combination of being
> an old git, having wrong locales and injecting self-attribution, was
> lethal. 

Does this mean the old version of git doesn't generate patches with the
correct locale?

I wonder... where is everyone getting git 2.1.4 from? It's 2 years old
;)

> 
> Pj.

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Sat, Feb 13, 2016 at 03:40:55PM -0500, Leo Famulari wrote:
> If that is it, then I believe git should "do the right thing" when
> generating patches. I've noticed that it progressively sets the encoding
> based on the minimum required to encode the characters in the patch.

The last line of your diffoscope shows that Pjotr's patch was encoded
in iso-8559-1, while all the scheme files in guix are in utf-8. It seems
quite clear to me that this is the reason for our problems. And apparently,
the git version plays a role in this.

Andreas

Re: [PATCH] gnu: Add slurm.

[Leo Famulari]

On Sun, Feb 14, 2016 at 03:22:56PM +0100, Andreas Enge wrote:
> On Sat, Feb 13, 2016 at 03:40:55PM -0500, Leo Famulari wrote:
> > If that is it, then I believe git should "do the right thing" when
> > generating patches. I've noticed that it progressively sets the encoding
> > based on the minimum required to encode the characters in the patch.
> 
> The last line of your diffoscope shows that Pjotr's patch was encoded
> in iso-8559-1, while all the scheme files in guix are in utf-8. It seems
> quite clear to me that this is the reason for our problems. And apparently,
> the git version plays a role in this.

I think the old version of git must play a role, or every patch with a
copyright attribution line would fail to apply.

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

[-- Attachment #1: Type: text/plain, Size: 371 bytes --]

On Sun, Feb 14, 2016 at 02:08:30PM -0500, Leo Famulari wrote:
> I think the old version of git must play a role, or every patch with a
> copyright attribution line would fail to apply.

New version cleaned up (using python-wrapper) and patch created
with latest git and en_US.utf8 Guix style...

Ah yes, lint is happy too. I am proud of this one. Hope you are.

Pj.

-- 

[-- Attachment #2: 0001-gnu-Add-slurm.patch --]
[-- Type: text/x-diff, Size: 6084 bytes --]

From 72513ea3f730323dc8977d97c9d4ddd691f6d48a Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Mon, 15 Feb 2016 10:14:44 +0000
Subject: [PATCH] gnu: Add slurm.

* gnu/packages/parallel.scm (slurm): New variable.
* gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch: New file.
* gnu/packages/parallel.scm (parallel): Introduce license name space.
---
 gnu-system.am                                      |  1 +
 gnu/packages/parallel.scm                          | 60 ++++++++++++++++++++--
 .../slurm-configure-remove-nonfree-contribs.patch  | 43 ++++++++++++++++
 3 files changed, 99 insertions(+), 5 deletions(-)
 create mode 100644 gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch

diff --git a/gnu-system.am b/gnu-system.am
index 91945db..7727bad 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -700,6 +700,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/slim-session.patch			\
   gnu/packages/patches/slim-config.patch			\
   gnu/packages/patches/slim-sigusr1.patch			\
+  gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch \
   gnu/packages/patches/soprano-find-clucene.patch		\
   gnu/packages/patches/sudo-CVE-2015-5602.patch			\
   gnu/packages/patches/superlu-dist-scotchmetis.patch		\
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 8f63bda..d6910de 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013,2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,12 +20,18 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages parallel)
-  #:use-module (guix packages)
-  #:use-module (guix licenses)
-  #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
   #:use-module (gnu packages)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tls))
 
 (define-public parallel
   (package
@@ -46,4 +53,47 @@
      "GNU Parallel is a tool for executing shell jobs in parallel using one
 or more computers.  Jobs can consist of single commands or of scripts
 and they are executed on lists of files, hosts, users or other items.")
-    (license gpl3+)))
+    (license license:gpl3+)))
+
+(define-public slurm
+  (package
+   (name "slurm")
+   (version "15.08.7.1")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/SchedMD/slurm/archive/slurm-"
+                  (string-join (string-split version #\.) "-") ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+             (base32
+              "1rmi35l4img00dr4vic8cv8s7b6n1yx1mkq2s7kjf5hvqdh6s2ki"))
+            (patches (list
+             (search-patch "slurm-configure-remove-nonfree-contribs.patch")))
+            (modules '((guix build utils)))
+            (snippet
+             '(begin
+                (delete-file-recursively "contribs")
+                #t))))
+   (inputs `(("openssl" ,openssl)
+             ("munge" ,munge)
+             ("perl" ,perl)
+             ("expect" ,expect)
+             ("python" ,python-wrapper)
+             ("linux-pam" , linux-pam)))
+   (native-inputs
+    `(("autoconf" ,autoconf)))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:configure-flags '("--enable-pam")
+      #:phases
+      (modify-phases %standard-phases
+       (add-before
+        'configure 'autogen
+        (lambda _ (zero? (system* "autoconf"))))))) ; configure.ac was patched
+   (home-page "http://slurm.schedmd.com/")
+   (synopsis "Workload manager for cluster computing")
+   (description
+    "Fault-tolerant and highly scalable cluster management and job
+scheduling system for large and small clusters.")
+   (license license:gpl2+)))
diff --git a/gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch b/gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch
new file mode 100644
index 0000000..b63d5bb
--- /dev/null
+++ b/gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch
@@ -0,0 +1,43 @@
+From 53eda9102b969a4be2882cea4befee03591a7436 Mon Sep 17 00:00:00 2001
+From: Pjotr Prins <pjotr.public01@thebird.nl>
+Date: Fri, 12 Feb 2016 12:43:33 +0100
+Subject: [PATCH] Remove contribs
+
+---
+ configure.ac | 20 --------------------
+ 1 file changed, 20 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index fedf354..e010732 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -438,26 +438,6 @@ dnl All slurm Makefiles:
+ AC_CONFIG_FILES([Makefile
+ 		 config.xml
+ 		 auxdir/Makefile
+-		 contribs/Makefile
+-		 contribs/cray/Makefile
+-		 contribs/cray/csm/Makefile
+-		 contribs/lua/Makefile
+-		 contribs/mic/Makefile
+-		 contribs/pam/Makefile
+-		 contribs/pam_slurm_adopt/Makefile
+-		 contribs/perlapi/Makefile
+-		 contribs/perlapi/libslurm/Makefile
+-		 contribs/perlapi/libslurm/perl/Makefile.PL
+-		 contribs/perlapi/libslurmdb/Makefile
+-		 contribs/perlapi/libslurmdb/perl/Makefile.PL
+-		 contribs/torque/Makefile
+-		 contribs/phpext/Makefile
+-		 contribs/phpext/slurm_php/config.m4
+-		 contribs/sgather/Makefile
+-		 contribs/sgi/Makefile
+-		 contribs/sjobexit/Makefile
+-		 contribs/slurmdb-direct/Makefile
+-		 contribs/pmi2/Makefile
+ 		 doc/Makefile
+ 		 doc/man/Makefile
+ 		 doc/man/man1/Makefile
+-- 
+2.1.4
+
-- 
2.6.3

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Mon, Feb 15, 2016 at 01:09:01PM +0100, Pjotr Prins wrote:
> New version cleaned up (using python-wrapper) and patch created
> with latest git and en_US.utf8 Guix style...

Well, it turned out it was still in iso-latin-1, and patching failed again...
Anyway, I applied the modifications and expanded the description a bit.

A number of configure flags were missing - without them, the inputs
would not be found in their non-standard location. I also added a
number of further inputs that seemed important to me.

I did not add all possible inputs. In particular, mysql and gtk+ (2 or 3?)
could be added, so it is possible that not all functionality is there.

The result is pushed to master.

Andreas

Re: [PATCH] gnu: Add slurm.

[Pjotr Prins]

On Mon, Feb 15, 2016 at 10:51:00PM +0100, Andreas Enge wrote:
> On Mon, Feb 15, 2016 at 01:09:01PM +0100, Pjotr Prins wrote:
> > New version cleaned up (using python-wrapper) and patch created
> > with latest git and en_US.utf8 Guix style...
> 
> Well, it turned out it was still in iso-latin-1, and patching failed again...
> Anyway, I applied the modifications and expanded the description a bit.

Weird. I should check that the files were utf8 before they went into
git. Maybe git is not the problem at all!

> A number of configure flags were missing - without them, the inputs
> would not be found in their non-standard location. 

Hmmm. It compiled, the tools ran...

> I also added a number of further inputs that seemed important to me.

Awesome!

Use of mysql or postgresql for detailed job information is optional.
By default it is text. I think it is fine this way, maybe we'll make
mysql a working option when we roll it out on our setup.

Pj.

Re: [PATCH] gnu: Add slurm.

[Andreas Enge]

On Tue, Feb 16, 2016 at 08:21:07AM +0100, Pjotr Prins wrote:
> > A number of configure flags were missing - without them, the inputs
> > would not be found in their non-standard location. 
> Hmmm. It compiled, the tools ran...

They probably concerned optional inputs, that maybe you did not need
in your use case; but since you had the inputs openssl and munge, it
made sense to activate them. The configure phase printed out warnings
about them missing.

> Use of mysql or postgresql for detailed job information is optional.
> By default it is text. I think it is fine this way, maybe we'll make
> mysql a working option when we roll it out on our setup.

I left a comment in the code so that people would be warned. So if you
or someone else finds a functionality that is missing, we might have
to add more inputs.

Andreas