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helo=www96.your-server.de X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Thu, 08 Jul 2021 16:43:26 -0400 X-BeenThere: help-guix@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: help-guix-bounces+larch=yhetil.org@gnu.org Sender: "Help-Guix" Reply-to: Sebastian Gibb From: Sebastian Gibb via X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1625777037; h=from:from:sender:sender:reply-to:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; 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dkim=fail ("headers rsa verify failed") header.d=sebastiangibb.de header.s=default_1812 header.b=scN1bWsm; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of help-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=help-guix-bounces@gnu.org X-Migadu-Queue-Id: EC71F13CB8 X-Spam-Score: -2.41 X-Migadu-Scanner: scn0.migadu.com X-TUID: cyn2Zy38r+3L Hi, I am trying to use `guix pack` to create a reproducible container that coul= d be used on an HPC. Unfortunately I am not able to schedule jobs from within the container or run any command from the host system. The HPC uses Cent OS 8.1. It offers slurm 20.02.5 for job scheduling and singularity 3.4.2 for virtualisation/own software bundles. I generated my container as follows: ``` cp $(/usr/local/bin/guix time-machine --commit=3Dc78d6c6 -- pack \ --relocatable --relocatable \ --format=3Dsquashfs \ --entry-point=3Dbin/bash \ --symlink=3D/bin=3Dbin \ --symlink=3D/lib=3Dlib \ --symlink=3D/share=3Dshare \ --save-provenance \ bash coreutils) mwe.squashfs ``` Next I try to use the host's `ssh` or slurms `sinfo`/`sbatch` from within t= he container but I got the error `No such file or directory`. Using `ls` or `c= at` I could access these files but I am not able to execute them: ``` SINGULARITY_BIND=3D"/usr" singularity run mwe.squashfs > /usr/bin/ssh runscript: /usr/bin/ssh: No such file or directory > ls /usr/bin/ssh /usr/bin/ssh > cat /usr/bin/ssh ELF>=EF=BF=BD@($ @8 ... ``` I could workaround the `ssh` problem by putting `openssh-sans-x` into the `guix pack` command and binding `/etc/group`, `/etc/passwd` and `/var/run` = to my singularity container. But if I include `slurm` I always got an error for `sinfo`/`sbatch`: "slurm_partitions: Zero Bytes were transmitted or received" (maybe I need to bind some more pathes to singularity?) 1. Is there a way to use the host commands from within the singularity/squa= shfs container generated by `guix pack`? 2. Or can I bind some more files/directory to my singularity command to get `slurm` commands working? By the way: I am not able to modify the PATH variable with `guix pack` gene= rated containers. It seems that SINGULARITY_PREPEND_PATH/SINGULARITY_APPEND_PATH = are ignored: ``` > SINGULARITY_PREPEND_PATH=3D"/usr/bin" \ singularity exec container/mwe.squashfs /bin/bash -c 'echo $PATH' WARNING: passwd file doesn't exist in container, not updating WARNING: group file doesn't exist in container, not updating /gnu/store/266jw5fcbygya3fkfbxkaa4yl23hrwci-profile/bin ``` 3. How to modify the PATH variable? (I know I could create a wrapper start script like `export PATH=3D$PATH:/usr/bin; /bin/bash` but even than I can't execute `ssh`/`sinfo`/`sbatch` and other host commands.) Best wishes, Sebastian