[bug#49167] [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls

[bug#49167] [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls

[Ryan Sundberg via Guix-patches via]

Disable the thread local storage model in jemalloc 5 to prevent
shared libraries linked to libjemalloc from crashing on dlopen().
https://github.com/jemalloc/jemalloc/issues/937

This bug affects both Java JNI and python libraries which link to
jemalloc 5, such as RocksDB, which will crash the program when loaded.

* gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls
configure flag.
---
 gnu/packages/jemalloc.scm | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm
index c4b87b540d..67a1ca8e14 100644
--- a/gnu/packages/jemalloc.scm
+++ b/gnu/packages/jemalloc.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2021 Ryan Sundberg <ryan@arctype.co>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,10 +30,10 @@
   #:use-module (gnu packages perl)
   #:use-module (guix build-system gnu))
 
-(define-public jemalloc
+(define jemalloc-4.5.0
   (package
     (name "jemalloc")
-    (version "5.2.1")
+    (version "4.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -40,7 +41,7 @@
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
+                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -58,7 +59,7 @@
            ;; Transparent huge pages are only enabled by default on Intel processors
            '()
            '(#:configure-flags (list "--disable-thp")))))
-    (inputs `(("perl" ,perl)))
+    (inputs '())
     ;; Install the scripts to a separate output to avoid referencing Perl and
     ;; Bash in the default output, saving ~75 MiB on the closure.
     (outputs '("out" "bin"))
@@ -69,10 +70,10 @@
 fragmentation avoidance and scalable concurrency support.")
     (license bsd-2)))
 
-(define-public jemalloc-4.5.0
+(define-public jemalloc
   (package
-    (inherit jemalloc)
-    (version "4.5.0")
+    (inherit jemalloc-4.5.0)
+    (version "5.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency support.")
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
-    (inputs '())))
+                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
+    (arguments
+      (substitute-keyword-arguments (package-arguments jemalloc-base)
+        ;; Disable the thread local storage model in jemalloc 5 to prevent
+        ;; shared libraries linked to libjemalloc from crashing on dlopen()
+        ;; https://github.com/jemalloc/jemalloc/issues/937
+        ((#:configure-flags base-configure-flags '())
+         `(cons "--disable-initial-exec-tls" ,base-configure-flags))))
+    (inputs `(("perl" ,perl)))))
-- 
2.31.1

[bug#49167] [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls

[Ryan Sundberg via Guix-patches via]

[-- Attachment #1.1.1: Type: text/plain, Size: 3683 bytes --]

Sorry, I missed a spot rebasing this last patch. Please use the attached
patch which builds.


--
Sincerely,
Ryan Sundberg

On 6/21/21 10:44 PM, Ryan Sundberg wrote:
> Disable the thread local storage model in jemalloc 5 to prevent
> shared libraries linked to libjemalloc from crashing on dlopen().
> https://github.com/jemalloc/jemalloc/issues/937
> 
> This bug affects both Java JNI and python libraries which link to
> jemalloc 5, such as RocksDB, which will crash the program when loaded.
> 
> * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls
> configure flag.
> ---
>  gnu/packages/jemalloc.scm | 26 +++++++++++++++++---------
>  1 file changed, 17 insertions(+), 9 deletions(-)
> 
> diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm
> index c4b87b540d..67a1ca8e14 100644
> --- a/gnu/packages/jemalloc.scm
> +++ b/gnu/packages/jemalloc.scm
> @@ -2,6 +2,7 @@
>  ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
>  ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
>  ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
> +;;; Copyright © 2021 Ryan Sundberg <ryan@arctype.co>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -29,10 +30,10 @@
>    #:use-module (gnu packages perl)
>    #:use-module (guix build-system gnu))
>  
> -(define-public jemalloc
> +(define jemalloc-4.5.0
>    (package
>      (name "jemalloc")
> -    (version "5.2.1")
> +    (version "4.5.0")
>      (source (origin
>                (method url-fetch)
>                (uri (string-append
> @@ -40,7 +41,7 @@
>                      version "/jemalloc-" version ".tar.bz2"))
>                (sha256
>                 (base32
> -                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
> +                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
>      (build-system gnu-build-system)
>      (arguments
>       `(#:phases
> @@ -58,7 +59,7 @@
>             ;; Transparent huge pages are only enabled by default on Intel processors
>             '()
>             '(#:configure-flags (list "--disable-thp")))))
> -    (inputs `(("perl" ,perl)))
> +    (inputs '())
>      ;; Install the scripts to a separate output to avoid referencing Perl and
>      ;; Bash in the default output, saving ~75 MiB on the closure.
>      (outputs '("out" "bin"))
> @@ -69,10 +70,10 @@
>  fragmentation avoidance and scalable concurrency support.")
>      (license bsd-2)))
>  
> -(define-public jemalloc-4.5.0
> +(define-public jemalloc
>    (package
> -    (inherit jemalloc)
> -    (version "4.5.0")
> +    (inherit jemalloc-4.5.0)
> +    (version "5.2.1")
>      (source (origin
>                (method url-fetch)
>                (uri (string-append
> @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency support.")
>                      version "/jemalloc-" version ".tar.bz2"))
>                (sha256
>                 (base32
> -                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
> -    (inputs '())))
> +                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
> +    (arguments
> +      (substitute-keyword-arguments (package-arguments jemalloc-base)
> +        ;; Disable the thread local storage model in jemalloc 5 to prevent
> +        ;; shared libraries linked to libjemalloc from crashing on dlopen()
> +        ;; https://github.com/jemalloc/jemalloc/issues/937
> +        ((#:configure-flags base-configure-flags '())
> +         `(cons "--disable-initial-exec-tls" ,base-configure-flags))))
> +    (inputs `(("perl" ,perl)))))
> 

[-- Attachment #1.1.2: 0001-gnu-jemalloc-disable-initial-exec-tls.patch --]
[-- Type: text/x-patch, Size: 3561 bytes --]

From a0f9f8206613efa659922f5164414832119a4d33 Mon Sep 17 00:00:00 2001
From: Ryan Sundberg <ryan@arctype.co>
Date: Fri, 29 Jan 2021 21:18:56 -0800
Subject: [PATCH] gnu: jemalloc: --disable-initial-exec-tls

Disable the thread local storage model in jemalloc 5 to prevent
shared libraries linked to libjemalloc from crashing on dlopen().
https://github.com/jemalloc/jemalloc/issues/937

This bug affects both Java JNI and python libraries which link to
jemalloc 5, such as RocksDB, which will crash the program when loaded.

* gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls
configure flag.
---
 gnu/packages/jemalloc.scm | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm
index c4b87b540d..67a1ca8e14 100644
--- a/gnu/packages/jemalloc.scm
+++ b/gnu/packages/jemalloc.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2021 Ryan Sundberg <ryan@arctype.co>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,10 +30,10 @@
   #:use-module (gnu packages perl)
   #:use-module (guix build-system gnu))
 
-(define-public jemalloc
+(define jemalloc-4.5.0
   (package
     (name "jemalloc")
-    (version "5.2.1")
+    (version "4.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -40,7 +41,7 @@
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
+                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -58,7 +59,7 @@
            ;; Transparent huge pages are only enabled by default on Intel processors
            '()
            '(#:configure-flags (list "--disable-thp")))))
-    (inputs `(("perl" ,perl)))
+    (inputs '())
     ;; Install the scripts to a separate output to avoid referencing Perl and
     ;; Bash in the default output, saving ~75 MiB on the closure.
     (outputs '("out" "bin"))
@@ -69,10 +70,10 @@
 fragmentation avoidance and scalable concurrency support.")
     (license bsd-2)))
 
-(define-public jemalloc-4.5.0
+(define-public jemalloc
   (package
-    (inherit jemalloc)
-    (version "4.5.0")
+    (inherit jemalloc-4.5.0)
+    (version "5.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency support.")
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
-    (inputs '())))
+                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
+    (arguments
+      (substitute-keyword-arguments (package-arguments jemalloc-base)
+        ;; Disable the thread local storage model in jemalloc 5 to prevent
+        ;; shared libraries linked to libjemalloc from crashing on dlopen()
+        ;; https://github.com/jemalloc/jemalloc/issues/937
+        ((#:configure-flags base-configure-flags '())
+         `(cons "--disable-initial-exec-tls" ,base-configure-flags))))
+    (inputs `(("perl" ,perl)))))
-- 
2.31.1


[-- Attachment #2: OpenPGP digital signature --]
[-- Type: application/pgp-signature, Size: 495 bytes --]

[bug#49167] [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls

[Ryan Sundberg via Guix-patches via]

[-- Attachment #1.1.1: Type: text/plain, Size: 3988 bytes --]

Please excuse my clumsiness, THIS is the fixed patch file. (I
accidentally re-sent the original patch.)

--
Sincerely,
Ryan Sundberg

On 6/21/21 10:52 PM, Ryan Sundberg via Guix-patches via wrote:
> Sorry, I missed a spot rebasing this last patch. Please use the attached
> patch which builds.
> 
> 
> --
> Sincerely,
> Ryan Sundberg
> 
> On 6/21/21 10:44 PM, Ryan Sundberg wrote:
>> Disable the thread local storage model in jemalloc 5 to prevent
>> shared libraries linked to libjemalloc from crashing on dlopen().
>> https://github.com/jemalloc/jemalloc/issues/937
>>
>> This bug affects both Java JNI and python libraries which link to
>> jemalloc 5, such as RocksDB, which will crash the program when loaded.
>>
>> * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls
>> configure flag.
>> ---
>>  gnu/packages/jemalloc.scm | 26 +++++++++++++++++---------
>>  1 file changed, 17 insertions(+), 9 deletions(-)
>>
>> diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm
>> index c4b87b540d..67a1ca8e14 100644
>> --- a/gnu/packages/jemalloc.scm
>> +++ b/gnu/packages/jemalloc.scm
>> @@ -2,6 +2,7 @@
>>  ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
>>  ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
>>  ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
>> +;;; Copyright © 2021 Ryan Sundberg <ryan@arctype.co>
>>  ;;;
>>  ;;; This file is part of GNU Guix.
>>  ;;;
>> @@ -29,10 +30,10 @@
>>    #:use-module (gnu packages perl)
>>    #:use-module (guix build-system gnu))
>>  
>> -(define-public jemalloc
>> +(define jemalloc-4.5.0
>>    (package
>>      (name "jemalloc")
>> -    (version "5.2.1")
>> +    (version "4.5.0")
>>      (source (origin
>>                (method url-fetch)
>>                (uri (string-append
>> @@ -40,7 +41,7 @@
>>                      version "/jemalloc-" version ".tar.bz2"))
>>                (sha256
>>                 (base32
>> -                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
>> +                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
>>      (build-system gnu-build-system)
>>      (arguments
>>       `(#:phases
>> @@ -58,7 +59,7 @@
>>             ;; Transparent huge pages are only enabled by default on Intel processors
>>             '()
>>             '(#:configure-flags (list "--disable-thp")))))
>> -    (inputs `(("perl" ,perl)))
>> +    (inputs '())
>>      ;; Install the scripts to a separate output to avoid referencing Perl and
>>      ;; Bash in the default output, saving ~75 MiB on the closure.
>>      (outputs '("out" "bin"))
>> @@ -69,10 +70,10 @@
>>  fragmentation avoidance and scalable concurrency support.")
>>      (license bsd-2)))
>>  
>> -(define-public jemalloc-4.5.0
>> +(define-public jemalloc
>>    (package
>> -    (inherit jemalloc)
>> -    (version "4.5.0")
>> +    (inherit jemalloc-4.5.0)
>> +    (version "5.2.1")
>>      (source (origin
>>                (method url-fetch)
>>                (uri (string-append
>> @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency support.")
>>                      version "/jemalloc-" version ".tar.bz2"))
>>                (sha256
>>                 (base32
>> -                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
>> -    (inputs '())))
>> +                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
>> +    (arguments
>> +      (substitute-keyword-arguments (package-arguments jemalloc-base)
>> +        ;; Disable the thread local storage model in jemalloc 5 to prevent
>> +        ;; shared libraries linked to libjemalloc from crashing on dlopen()
>> +        ;; https://github.com/jemalloc/jemalloc/issues/937
>> +        ((#:configure-flags base-configure-flags '())
>> +         `(cons "--disable-initial-exec-tls" ,base-configure-flags))))
>> +    (inputs `(("perl" ,perl)))))
>>

[-- Attachment #1.1.2: 0001-gnu-jemalloc-disable-initial-exec-tls.patch --]
[-- Type: text/x-patch, Size: 3562 bytes --]

From 8b97b60ab78ba1e616efaf477e629cfa2457b1a9 Mon Sep 17 00:00:00 2001
From: Ryan Sundberg <ryan@arctype.co>
Date: Fri, 29 Jan 2021 21:18:56 -0800
Subject: [PATCH] gnu: jemalloc: --disable-initial-exec-tls

Disable the thread local storage model in jemalloc 5 to prevent
shared libraries linked to libjemalloc from crashing on dlopen().
https://github.com/jemalloc/jemalloc/issues/937

This bug affects both Java JNI and python libraries which link to
jemalloc 5, such as RocksDB, which will crash the program when loaded.

* gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls
configure flag.
---
 gnu/packages/jemalloc.scm | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm
index c4b87b540d..d93cf41081 100644
--- a/gnu/packages/jemalloc.scm
+++ b/gnu/packages/jemalloc.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2021 Ryan Sundberg <ryan@arctype.co>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,10 +30,10 @@
   #:use-module (gnu packages perl)
   #:use-module (guix build-system gnu))
 
-(define-public jemalloc
+(define jemalloc-4.5.0
   (package
     (name "jemalloc")
-    (version "5.2.1")
+    (version "4.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -40,7 +41,7 @@
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
+                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -58,7 +59,7 @@
            ;; Transparent huge pages are only enabled by default on Intel processors
            '()
            '(#:configure-flags (list "--disable-thp")))))
-    (inputs `(("perl" ,perl)))
+    (inputs '())
     ;; Install the scripts to a separate output to avoid referencing Perl and
     ;; Bash in the default output, saving ~75 MiB on the closure.
     (outputs '("out" "bin"))
@@ -69,10 +70,10 @@
 fragmentation avoidance and scalable concurrency support.")
     (license bsd-2)))
 
-(define-public jemalloc-4.5.0
+(define-public jemalloc
   (package
-    (inherit jemalloc)
-    (version "4.5.0")
+    (inherit jemalloc-4.5.0)
+    (version "5.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency support.")
                     version "/jemalloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))))
-    (inputs '())))
+                "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))))
+    (arguments
+      (substitute-keyword-arguments (package-arguments jemalloc-4.5.0)
+        ;; Disable the thread local storage model in jemalloc 5 to prevent
+        ;; shared libraries linked to libjemalloc from crashing on dlopen()
+        ;; https://github.com/jemalloc/jemalloc/issues/937
+        ((#:configure-flags base-configure-flags '())
+         `(cons "--disable-initial-exec-tls" ,base-configure-flags))))
+    (inputs `(("perl" ,perl)))))
-- 
2.31.1


[-- Attachment #2: OpenPGP digital signature --]
[-- Type: application/pgp-signature, Size: 495 bytes --]

bug#49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls

[Ludovic Courtès]

Hi Ryan,

Ryan Sundberg <ryan@arctype.co> skribis:

> From 8b97b60ab78ba1e616efaf477e629cfa2457b1a9 Mon Sep 17 00:00:00 2001
> From: Ryan Sundberg <ryan@arctype.co>
> Date: Fri, 29 Jan 2021 21:18:56 -0800
> Subject: [PATCH] gnu: jemalloc: --disable-initial-exec-tls
>
> Disable the thread local storage model in jemalloc 5 to prevent
> shared libraries linked to libjemalloc from crashing on dlopen().
> https://github.com/jemalloc/jemalloc/issues/937
>
> This bug affects both Java JNI and python libraries which link to
> jemalloc 5, such as RocksDB, which will crash the program when loaded.
>
> * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls
> configure flag.

It took a long while, but it’s now in ‘core-updates-frozen’ as
68dd6d809398297dc2ebef522186c9b9f2566739 (with minor tweaks so it would
apply and so that ‘jemalloc-4.5.0’ remains public.)

Thanks!

Ludo’.

[bug#49167] closed (Re: bug#49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls)

[Ryan Sundberg via Guix-patches via]

[-- Attachment #1.1: Type: text/plain, Size: 498 bytes --]

Awesome. Thanks Ludo. This will unblock the rocksdb-java package I've
been sitting on.

--
Sincerely,
Ryan Sundberg

On 9/3/21 3:07 AM, GNU bug Tracking System wrote:
> Your bug report
> 
> #49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls
> 
> which was filed against the guix-patches package, has been closed.
> 
> The explanation is attached below, along with your original report.
> If you require more details, please reply to 49167@debbugs.gnu.org.
> 


[-- Attachment #2: OpenPGP digital signature --]
[-- Type: application/pgp-signature, Size: 495 bytes --]