Tag: SLURM

[slurm-users] How to launch slurm services after installation

Hello, all supported build flags are available with “./configure –help” command. On of them is “–with-systemdsystemunitdir=DIR”, which will allow you to specify the directory for the systemd service files for all Slurm daemons. The most important of the flags is imho the “–prefix”, which sets the installation directory. I’ll describe my build setup shortly…

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Bioinformatics Analyst II – Epigenetics & 3D Genomics Job in Texas

Summary The lab of Dr. Kyle Eagen (www.eagenlab.org) at Baylor College of Medicine focuses on elucidating how DNA folds within cells and how DNA misfolding relates to human disease. Baylor College of Medicine, one of the top ranked medical schools in the country, is well known for its exceptional,…

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Parallel Computing Toolbox plugin for MATLAB Parallel Server with Slurm – File Exchange

Installer file for Parallel Computing Toolbox plugin for MATLAB Parallel Server with Slurm. These example files use the generic scheduler interface to enable users to submit jobs to MATLAB Parallel Server with Slurm. Once installed, you will need to perform further steps before the scheduler is ready to use. For…

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Sbatch How Submitted Location Using Jobid With Code Examples

Sbatch How Submitted Location Using Jobid With Code Examples With this piece, we’ll take a look at a few different examples of Sbatch How Submitted Location Using Jobid issues in the computer language. scontrol show job your_job_id_234533 We learned how to solve the Sbatch How Submitted Location Using Jobid by…

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Completed: Quarterly Cluster Maintenance Tuesday October 25 | crc.pitt.edu

Dear CRC User Community, We have completed our quarterly maintenance and have returned the clusters to production. The key changes to the CRC clusters are the following: Storage Systems updates – Improved performance of iX with cache upgrades SLURM Workload Manager –  Update to newest version (22.05) Due to incompatibility between…

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ThompsonA93/C-Slurm-Benchmark: C sequential/parallel programming benchmark

GitHub – ThompsonA93/C-Slurm-Benchmark: C sequential/parallel programming benchmark This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You…

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Install Sview On A Debian, Ubuntu, Kali, Fedora And Raspbian

sview GUI to view and modify SLURM state Maintainer: Debian HPC Team Section: admin Install sview Debian apt-get install sview Click to copy Ubuntu apt-get install sview Click to copy Kali Linux apt-get install sview Click to copy Fedora dnf install sview Click to copy Raspbian apt-get install sview Click…

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Get stdout/stderr from a slurm job at runtime

I have a batch file to send a job with sbatch.The contents of the batch file is # Setting the proper SBATCH variables … #SBATCH –error=”test_slurm-%j.err” #SBATCH –output=”test_slurm-%j.out” … WORKDIR=. echo “Run 1” ${WORKDIR}/test_slurm echo “Run 2” ${WORKDIR}/test_slurm File test_slurm-%j.out is sometimes appended with output only after each of the…

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ACENET Basics: Job Scheduling with Slurm Tickets, Fri, 23 Sep 2022 at 10:00 AM

This session teaches participants how to use the Digital Research Alliance of Canada’s queuing environment on the national systems, using the job scheduler Slurm. Learn how the scheduler works, how it allocates jobs, what are reasonable requests to minimize wait time, how to make the best use of the resources…

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Why is the wrong queue being selected when submitting a job to my cluster using a Slurm scheduler? – MATLAB Answers

My workflow consists of submitting jobs to my cluster which is using Slurm as the scheduler. I am trying to target a specific queue/partition on my Slurm scheduler. I have used ‘AdditionalProperties’ to set the queue to the desired one via the following: c = parcluster(‘<CLUSTER_NAME>’) c.AdditionalProperties.Partition = ‘<PARTITION>’ c.AdditionalProperties.QueueName…

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How to activate a specific Python environment as part of my submission to Slurm?

You mean to activate a specific Python environment as part of your submission to Slurm? This is what I add to my job script and it works well. Note that I use Anaconda, which by default adds the required paths to my .bashrc script after installation. Hope this helps. …….

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Index of /ubuntu/pool/universe/s/slurm-drmaa

Name Last modified Size Description Parent Directory   –   slurm-drmaa-dev_1.0.6-2build3_amd64.deb 2014-01-20 15:43 8.2K   slurm-drmaa-dev_1.0.6-2build3_i386.deb 2014-01-20 15:43 8.1K   slurm-drmaa-dev_1.0.7-1build3_amd64.deb 2016-01-05 06:56 8.1K   slurm-drmaa-dev_1.0.7-1build3_i386.deb 2016-01-05 06:56 8.1K   slurm-drmaa1_1.0.6-2build3_amd64.deb 2014-01-20 15:43 51K   slurm-drmaa1_1.0.6-2build3_i386.deb 2014-01-20 15:43 49K   slurm-drmaa1_1.0.7-1build3_amd64.deb 2016-01-05 06:56 51K   slurm-drmaa1_1.0.7-1build3_i386.deb 2016-01-05 06:56 58K  …

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Running parfor on SLURM limits cores to 1 – MATLAB Answers

Hello, I’m trying to run some parallelized code (through parfor) on a university high performance cluster. In order to make sure parallelization is working correctly, I set up a single node with 32 cores via “srun –pty -t 00:30:00 -n 32 -N 1 /bin/bash -l”, which I verify does start…

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Futurama Hit & Run Is Making My Childhood Dreams Come True

You’ve played Simpsons Hit & Run, but what if it was set in the year 3000? There’s only been one Futurama game (if you don’t include the freemium mobile game), and that’s Futurama for the PlayStation 2. A third-person platformer developed by Unique Development Studios, Futurama for the PlayStation 2 received middling…

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Cornell Virtual Workshop: Execution: idev (at TACC)

TACC also offers their idev command (for interactive development) as a convenient way to initiate interactive work on their compute nodes, via Slurm. It works very much like srun and even takes many of the same options. But by making a few assumptions, idev shortens the path for you…

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Slurm Thrower | RIPT Apparel

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Transition from Woody with Ubuntu 18.04 and Torque to Woody-NG with AlmaLinux8 and Slurm

2022-07-17 Valued Tier3 HPC users of NHR@FAU, as briefly announced in the HPC Cafe in June, we now started with switching from Woody with Ubuntu 18.04 and Torque to Woody-NG (“Woody Next Generation”) with AlmaLinux8 as operating system and Slurm as batch system. Woody-NG uses the same operating system as…

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Sr. Bioinformatics-Clinical Database Developer – CBL Path, Inc

Job Functions, Duties, Responsibilities and Position Qualifications: POSITION TITLE:Senior Bioinformatics-Clinical Database Developer STANDARDIZED JOB TITLE: Database Development, Web Application Development, and Clinical Analytics EXEMPT STATUS:  Exempt POSITION SUMMARY: Sr. Database Developer works with cross-functional groups & Medical Leadership for developing a databases for a clinical assays. The candidate is expected…

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Bug#1014506: slurm-wlm: flaky autopkgtest: sbatch fails without

Source: slurm-wlm Version: 21.08.8.2-1 Severity: serious X-Debbugs-CC: debian…@lists.debian.org User: debian…@lists.debian.org Usertags: flaky Dear maintainer(s), I looked at the results of the autopkgtest of you package on armhf because it was showing up as a regression for the upload of perl. I noticed that the test regularly fails and I saw…

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[slurm-users] “Plugin is corrupted” message when using drmaa / debugging libslurm

On 28/06/2022 23:14, Chris Samuel wrote: > On 28/6/22 12:19 pm, Jean-Christophe HAESSIG wrote: Hi, Yes I also found it and that’s where I saw the detailed debug3 & debug4 calls. > it’s when it’s checking it can load the plugin and not hit any > unresolved library symbols. The…

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mpi – slurm can’t execute srun

slurm cannot run srun -n 1 /home/user/share/test/hello.o is ok rpi40000: 0 of 1 but srun -n 2 /home/user/share/test/hello.o is error. srun: error: slurm_receive_msgs: Socket timed out on send/recv operation srun: error: Task launch for StepId=53.0 failed on node rpi40001: Socket timed out on send/recv operation srun: error: Application launch failed:…

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Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member Location: EMBL-EBI, Hinxton near Cambridge, UK Job Function: Senior Technical Officer (gr. 6-8) Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023) Contract Duration-Is this renewable to 9 years?: No Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits) About the team/job We are seeking…

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Index of /~ckern/FAANG_Project/Cattle_NCBI

Name Last modified Size Description Parent Directory   –   Aligned_Reads/ 2016-07-30 04:38 –   Cufflinks_Output/ 2017-11-11 11:53 –   FEELnc/ 2018-08-14 16:03 –   Gene_Expression/ 2016-09-01 14:14 –   Genome/ 2018-04-04 15:54 –   Intermediate_LncRNA.feelncclassifier.log 2016-08-05 15:59 18K   LncRNA/ 2018-08-08 11:07 –   Raw_Reads/ 2016-07-28 15:11 –  …

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A few resources to help enable using Distributed.jl on a SLURM cluster – Specific Domains

jmair May 30, 2022, 11:38am #1 I created some resources for a few colleagues new to Julia, to enable them to use our SLURM cluster effectively, using existing packages like Distributed.jl and ClusterManagers.jl. These scripts and resources do nothing novel or imaginative, and are more of an example of how…

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Slurm Cola Ice Blue Unisex Hoodie

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Sweeps while using MPI and SLURM – W&B Support

Hello! I am attempting to perform a hyperparameter search on my project, which uses MPI under the hood to aggregate the results of multiple agents. I have 63 agents that run an episode, returning a total reward at the end. At the end, each worker node sends their results to…

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SchedMD Slurm privilege escalation | CVE-2022-29501

NAME SchedMD Slurm privilege escalation Platforms Affected:SchedMD Slurm 20.11.6SchedMD Slurm 20.02.6 Risk Level:9.8 Exploitability:Unproven Consequences:Gain Privileges DESCRIPTION SchedMD Slurm could allow a remote attacker to gain elevated privileges on the system, caused by improper access control in a network RPC handler in the slurmd daemon used for PMI2 and PMIx…

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[slurm-users] gres/gpu count lower than reported

Hello Fellow Slurm Admins,   I have a new Slurm installation that was working and running basic test jobs until I added gpu support. My worker nodes are now all in drain state, with gres/gpu count reported lower than configured (0 < 4)   This is in spite of the…

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Distributed training on slurm cluster – distributed

chinmay5 (Chinmay5) April 29, 2022, 12:48pm #1 Sorry for the naive question but I am confused about the integration of distributed training in a slurm cluster. Do we need to explicitly call the distributed.launch when invoking the python script or is this taken care of automatically? In other words, is…

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Slurm: Stdout and stderr log files

-e, –error=<filename pattern> Instruct Slurm to connect the batch script’s standard error directly to the file name specified in the “filename pat‐ tern”. By default both standard output and standard error are directed to the same file. For job arrays, the default file name is “slurm-%A_%a.out”, “%A” is replaced by…

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Slurm pending jobs – Stack Overflow

i have a problem with slurm every job i execute keeps pending and i dont know what to do (im new to the field) scontrol: show job JobId=484 JobName=Theileiria_project UserId=dhamer(1037) GroupId=Bio-info(1001) MCS_label=N/A Priority=4294901741 Nice=0 Account=(null) QOS=normal JobState=PENDING Reason=BeginTime Dependency=(null) Requeue=1 Restarts=481 BatchFlag=1 Reboot=0 ExitCode=0:0 RunTime=00:00:00 TimeLimit=01:00:00 TimeMin=N/A SubmitTime=2022-04-19T08:47:58 EligibleTime=2022-04-19T08:49:59 AccrueTime=2022-04-19T08:49:59…

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Slurm drinks Vending machine – General Chat

Slurm drinks Vending machine – General Chat – Aussie Arcade Jump to content Read more here: Source link

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[slurm-users] Issues with pam_slurm_adopt

Hi, I have an issue with pam_slurm_adopt when I moved from 21.08.5 to 21.08.6. It no longer works. When I log straight to the node with root account : Apr 8 19:06:49 magi46 pam_slurm_adopt[20400]: Ignoring root user Apr 8 19:06:49 magi46 sshd[20400]: Accepted publickey for root from 172.16.0.3 port 50884 ssh2:…

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Problem with Python environment and Slurm (srun/sbatch)

I had a similar issue with Slurm Version 20.11.7I had a virtual environment created with the systems python3, which was Python 3.6.8When activating the venv on the logging-node calling an installed module worked fine, but from within the following shell script for example it did not and resulted in ModuleNotFound:…

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Can a user restrict a slurm job to only run on specific GPUS?

I have a workstation with 4 GPUs. I’ve setup my machine as a single-node slurm instance. I use slurm to automate complex job pipelines in the background while I work in the foreground. So I’m not doing much HPC, I’m just using SLURM to handle job DAGs. I have a…

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slurm – How is RealMemory (slurmd -C) calculated? Why does it differ from MemTotal?

The SLURM documentation says RealMemory Size of real memory on the node in megabytes (e.g. “2048”). The default value is 1. Lowering RealMemory with the goal of setting aside some amount for the OS and not available for job allocations will not work as intended if Memory is not set…

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[Solved] Use Bash variable within SLURM sbatch script

This won’t work. What happens when you run sbatch myscript.sh is that slurm parses the script for those special #SBATCH lines, generates a job record, stores the batch script somewhere. The batch script is executed only later when the job runs. So you need to structure you workflow in a…

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Accepted slurm-wlm 21.08.6-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 22 Mar 2022 21:59:40 +0100 Source: slurm-wlm Architecture: source Version: 21.08.6-1 Distribution: unstable Urgency: medium Maintainer: Debian HPC Team <debian-…@lists.debian.org> Changed-By: Gennaro Oliva <oliv…@na.icar.cnr.it> Changes: slurm-wlm (21.08.6-1) unstable; urgency=medium . * New upstream release * Remove fix-typos patch included upstream…

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Futurama: Hit & Run – Teaser trailer #1 | Topic

Slurm Team Good News everyone! Further information to be revealed shortly! Good News everyone! Further information to be revealed shortly! ImmortalFlamixGod Wow, I’m so hyped! snipergaming i.imgur.com/kktw9mN.gif Freelancer_T_O_T Yes! This is what I’ve been waiting for! I hope that classic Futurama Intro is played straight after the…

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Git/SVN Repository and Slurm based Job Management – Freelance Job in Network & System Administration – $100 Fixed Price, posted March 20, 2022

A) GIT/SVN :- We need to set-up a git or svn repository and client systems. Following are the gist – 1) The (Git/SVN) repository will run in CentOS 7 based server. 2) Multiple (GIT/SVN) clients will run from same machine and access this repository. Will source/submit to them. This is…

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Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

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How do I get SLURM to allocate jobs to all CPUs

I’m trying to run an array job with the configuration below. My nodes have 4 cpu, but the scheduler is only allocating two jobs per node. How can I get it to allocate four jobs per node? When I add #SBATCH –ntasks-per-node=4, it’s even worse – I get one task…

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[slurm-users] Performance with hybrid setup

Hello, I’m performing some tests (CPU-only systems) in order to compare MPI versus hybrid setup. The system is running OpenMPIv4.1.2 so that a job submission reads:       mpirun -np 48 foo.exe or       export OMP_NUM_THREADS=8       mpirun -np 6 foo.exe In our system, the latter runs slightly faster (about 5…

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Error in creating cyclecloud cluster (No nodes found for nodearray hpc)

Hello, I’m trying to setup my first CycleCloud cluster, but I keep getting error in the initialization phase. In particular, it complains about not finding nodes for “nodearray hpc”. The full error message: CycleCloud Version: 8.2.0-1616 Cluster: Test2 (version 8.2.x) ============================== Status: Error [Software Configuration] (retrying) Start Time: 2022-03-13T17:31:29.377Z Description:…

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[slurm-users] Reserving slots with sbatch and OpenMpi

With sbatch, what is the proper way to launch 5 tasks each on a single node, but reserve two slots on each node so that the original tasks can each create one new process using MPI_Comm_spawn?   I’ve tried various combinations of the sbatch arguments –nodes, –ntasks-per-node and –cpu-per-node, but…

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Unable to run python script from bash scripts with string arguments : SLURM

I want to run it from a bash script but it is not accepting string input with spaces. It works with single words or hyphenated words. However the python command is correct and is working fine when I am running it directly from terminal. commands.txt python generate.py -p “Flower girl”…

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Space Smoke 30g Berry Slurm

Return and Refund Policy Thank you for shopping at Smoxygen Inc. If, for any reason, You are not completely satisfied with a purchase We invite You to review our policy on refunds and returns. The following terms are applicable for any products that You purchased with Us. Interpretation and Definitions…

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[slurm-users] Slurm-PMIx integration

Current Slurm official repository branches contain only a limited PMIx integration, primarily constrained to providing support for the traditional put-get exchange of key-value pairs. The support is also restricted to PMIx v3.x releases and below, though this restriction is due to a configure limitation as opposed…

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[slurm-users] step creation temporarily disabled, retrying (Requested nodes are busy)

I have a slurm cluster on centos7 installed through yum, I also have mpich installed. However I can’t make it work through slurm, these are the logs form running the job: # srun –mpi=pmi2 -N3 -vvv /usr/lib64/mpich/bin/mpirun /scratch/mpi-helloworld srun: defined options srun: ——————– ——————– srun: mpi    …

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Passing a parameter into a slurm script (matlab)

I am using slurm to submit jobs to the university supercomputer. My matlab function has one parameter: function test(variable_1) and my slurm file is (I am not sure if it is correct. I know how to define the value of the parameter in the slurm file, but I would like…

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Request exclusive use of slurm batch nodes for a parpool that is less than the total number of cores. –

Hi, is there a way to tell a slurm matlab job to run in exclusive mode on 2 nodes even though the parpool is using fewer than the total number of cores? Our slurm batch nodes have 128 cores, but I am only requesting a parpool of 240, but I…

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[slurm-users] mps on A100 only zero-index GPU was used when there is four GPUs

Hi threre, I was testing the MPS on Slurm19.05.5 with 4 A100 in compute node. In my opinion, the 4 A100 will be used.  But I found that only the first GPU was used. like below: the job script: #!/bin/bash #SBATCH -J date #SBATCH -p NVIDIAA100-PCIE-40GB #SBATCH -n 1 #SBATCH…

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how to create temporary folders in a slurm script hpc script code example

Example: how to create temporary folders in a slurm script hpc script #!/bin/bash #SBATCH –job-name=sand_min #SBATCH -N 1 #SBATCH -n 1 ##SBATCH –gres=gpu:1 #SBATCH –partition=shortq7 #SBATCH –exclude=node[007,041,046],nodeamd[010-014],nodeeng[009-010],nodegpu001,nodenviv[100001-100002,100004-100015] #SBATCH –mail-type=ALL #SBATCH –time=6:00:00 echo “NODE NAMES = “$SLURM_NODELIST echo “CUDA_VISIBLE_DEVICES = “$CUDA_VISIBLE_DEVICES date # # Load the necessary modules, etc… # module…

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[slurm-users] DefaultQOS not set for cluster when running sacctmgr load file

For some reason it seems that DefaultQOS does not get set on the cluster level when loading from file? Any ideas on why or if I have something wrong? I’ve removed some output below for simplicity. As you can see below it is added when doing sacctmgr modify cluster cluster…

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awk – Submitting a job in Slurm using wrap

I am trying to create an automatic chain of commands for analyzing biological data. For this I am using Samtools in Slurm cluster. This line below is one of the commands I run for the analysis: samtools view -h file.sam | awk ‘$6 ~ /N/ || $1 ~ /^@/’ |…

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[slurm-users] Issues upgrading db from 20.11.7 -> 21.08.4

Hello! I’m trying to test an upgrade of our production slurm db on a test cluster. Specifically I’m trying to verify a update from 20.11.7 to 21.08.4. I have a dump of the production db, and imported as normal. Then firing up slurmdbd to perform the conversion. I’ve verified everything…

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permissions – How to limit cluster users from using GPU resources without SLURM

I currently have a single node with 4 GPUs. I’ve configured SLURM such that the default profile in /etc/profile.d/ has CUDA_VISIBLE_DEVICES=-1 which prevents users from running jobs on GPUs without going through SLURM directly. However this disables salloc functionality, and users cannot use salloc to interactively reserve GPUs for a…

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[slurm-users] Fairshare within a single Account (Project)

You can. We use:   sacctmgr show assoc where account=researchgroup format=user,share   to see current fairshare within the account, and:                   sacctmgr modify user where name=someuser account=researchgroup set fairshare=N   to modify a particular user’s fairshare within the account.   External Email Warning This email originated from outside…

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Slurm environment variable for requested time

For a slurm job, the environment variable $SLURM_JOB_NUM_NODES gives the number of nodes requested. Is there a similar variable that gives the run time requested? I couldn’t find the answer and I have tried $SLURM_JOB_TIME, $SLURM_TIME and $SLURM_SUBMIT_TIME, but none of these works. Ultimate goal is to let the script…

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parallel processing – Forcing subsequent SLURM jobs to wait until first job is done?

I am running 1000 jobs on a cluster, using a sbatch job array. I’ve set up my code such that if the job array index is set to 0, precomputations are executed and saved to file; the jobs 1-999 then access these precomputations. The precomputations in job 0 take much…

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How do I save print statements when running a program in SLURM?

By default, print in Python is buffered, meaning that it does not write to files or stdout immediately, and needs to be ‘flushed’ to force the writing to stdout immediately. See this question for available options. The simplest option is to start the Python interpreter with the -u option. From…

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[pytorch/torchx] slurm: environment improvements

The current slurm scheduler specifies the working directory via the image field of the Role. This doesn’t match how any of the other schedulers work since local_cwd has been switched to use the current working directory. We should update the slurm scheduler to be more inline with the other schedulers….

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r – How to parallelize future_pmap() across multiple slurm nodes

I have access to a large computing cluster with many nodes each of which has >16 cores, running Slurm 20.11.3. I want to run a job in parallel using furrr::future_pmap(). I can parallelize across multiple cores on a single node but I have not been able to figure out the…

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Simplify your life with SLURM and sync

For my first blog post of the year, we’re talking about SLURM, everyone’s favorite job manager. If like me, you have the joy of running a literal boat-load of jobs with all kinds of parameters and command-line arguments you’ll know there are a few tips and tricks that make the…

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[slurm-users] Questions about scontrol reconfigure / reconfig

Hello, I have some questions about adding nodes in configless mode. My version of SLURM is 21.08.5. I gave logs below to ease the read of the message. First, is “scontrol reconfigure” equal to “scontrol reconfig” ? Then, I have a strange behaviour at node addition. I have an healthy…

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[slurm-users] Strange sbatch error with 21.08.2&5

Running test job with srun works: wayneh@login:~$ srun -G16 -p v100 /home/wayne.hendricks/job.sh 179851 Linux dgx1-1 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 179851 Linux dgx1-2 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Submitting the same with sbatch does…

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Question: total memory usage (–mem) exceeded the RealMemory in pcluster with SLURM

Hello, I have set RealMemory=58000 (though they are 64G instances) in the file slurm_parallelcluster_queue_partition.conf When I run the following commands: sbatch -N 1 -n 1 –mem=40000 –wrap=”srun script.sh first_task” sbatch -N 1 -n 1 –mem=40000 –wrap=”srun script.sh second_task” and more They will be assigned to single instance which lead to…

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Running Jobs on Titan

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

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runing a command multiple times in different nodes in SLURM

I want to run three instances of GROMACS mdrun on three different nodes. I have three temperatures 200,220 and 240 K and I want to run 200 K simulation on node 1, 220 K simulation on node 2 and 240 K simulation on node 3. I need to do all…

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biopython – Github Help

1 1 0 biopython,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

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kegg – Github Help

1 1 0 kegg,How to rescue failed project ? To do: 1. The wrapper of the KEGG gene orthology database should obtain gene names. 2. Pandas should be replaced by other software more appropriate for data mining by counting lines in tables ( see towardsdatascience.com/surprising-sorting-tips-for-data-scientists-9c360776d7e). i User: dariusz-izak-doktorat pandas python…

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Installation times out – githubmate

I’m not able to get this running. The cloud formation template times out with this step seemingly the problem: SlurmManagementEC2WaitCondition | im-slurm-2-SlurmManagementEC2WaitCondition-PNDUOLXY4N9W | AWS::CloudFormation::WaitCondition | CREATE_IN_PROGRESS | Resource creation Initiated Details: Region: eu-central-1 AMI: ami-0e8286b71b81c3cc1 Slurm version: 20.02.5 It seems that the slurm binaries get created but slurm never becomes…

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Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage?

Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage? 1 I am using a SLURM HPC to run jobs and have ran into issues with storage. I have 3TB storage, and want to run over 1000 publicly available RNAseq data through my pipeline, which includes…

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How does slurm work? – IT & Software development Q&A

Hi, I was relatively recently told about slurm, however, as usual, I did not have time to go into details and had to quickly write scripts and subsample them “to not waste time”. Well, since recently, constantly goes out of timeout and scripts “do not finish” as simply not enough…

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SLURM and tailoring walltime for different jobs –

Hi, so finally, I have access to a big cluster that uses SLURM as scheduler for Matlab. So far so good. Now, I would need to understand if I am planning the execution of my program properly. I have a Main file, with several batch jobs. At the moment, it…

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Install Slurm 19.05 on a standalone machine running Ubuntu 20.04

Use apt to install the necessary packages: sudo apt install -y slurm-wlm slurm-wlm-doc Load file:///usr/share/doc/slurm-wlm/html/configurator.html in a browser (or on WSL2), and: 1. Set your machine’s hostname in `SlurmctldHost` and `NodeName`. 2. Set `CPUs` as appropriate, and optionally `Sockets`, `CoresPerSocket`, and `ThreadsPerCore`. Use command `lscpu` to find what you…

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docker – SLURM cluster inside k8s cannot run srun command

I’m a beginner k8s user, I’m trying to recreate this docker-compose SLURM cluster with kubernetes. First I converted the docker-compose.yaml file into k8s yaml file in order to use kubectl apply -f . to create pods and services. I’m using minikube on my computer with the none driver (like this…

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Webinar: Batch System at OSC

OSC will host a webinar on the SLURM batch system on Owens and Pitzer, on January 19, 2022, from 1:00pm to 3:00pm. We will discuss SLURM syntax and go through hands-on activities on submitting, running, and managing jobs on the clusters using SLURM batch scripts and interactive batch sessions. Who…

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How to make SLURM use gres.conf

I distribute jobs using SLURM, and I have a generic resource called “cards”. In slurm.conf there is a line: GresTypes=cards I do not include this resource in the node configuration lines. Instead, I try and configure it in gres.conf: NodeName=mynode-01 Name=cards Count=2 Unfortunately, scontrol show node mynode-01 shows Gres=(null). Both…

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[workshop] Building HPC clusters with LXD, Slurm & GPU:s – community-workshop

Welcome to join another exciting community workshop with Juju and related projects! This time @mmrezaie will take us through an interesting deployment of Slurm charms to build a HPC cluster with juju and lxd. Meeting link: meet.google.com/ceh-zber-jnf Date: Fri 2021-12-17 09:00 – 10:00 (UTC) Abstract In this workshop we will…

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How to get count of failed and completed jobs in an array job of slurm ( Slurm, Sbatch )

Problem : ( Scroll to solution ) I am running multiple array jobs using slurm. For a given array job id, let’s say 885881, I want to list the count of failed and completed number of jobs. Something like this: Input: <some-command> -j 885881 Output: Let’s say we have 200…

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NoMachine Forums – NoMachine and slurm created cgroups

Hello everyone, We installed NoMachine on clusters we use remotely. These clusters are handled with a scheduler called slurm. Every time a user allocate a node with slurm, its session enters a cgroup which bounds the resources the user can use. Slurm allows for example one user to use a…

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[slurm-users] smap on Centos7

Hi, This is my first post. :-) Where can I find the ‘smap’ gui for Cenos7 ? I can’t seem to locate the package that provides this. I didn’t get any results with ‘yum whatprovides smap’. In contrast, ‘yum whatprovides sview’ gives me ‘slurm-gui’. Shouldn’t smap be part of…

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Running SortMeRNA on Multiple Files

Running SortMeRNA on Multiple Files 0 Hi all, I am VERY new to SortMeRNA (I’m a PhD student taking a bioinformatics class that has been very poorly taught). I have 27 paired samples for a total of 54 samples named like this: SRR13711719_1_val_1.fq SRR13711719_2_val_2.fq. So the format is _1_val_1.fq and…

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Slurm installation for multiple users – Install, Configure and Update

Welcome to the forum @bzuber.As you already suspected, jobs submitted through the web UI are counted against the quota of the system user that owns the cryoSPARC instance. Cluster resources and quota need to be allocated according to the combined needs of all cryoSPARC users. You may still capture information…

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[slurm-users] A Slurm topological scheduling question

Hi David, The topology.conf file groups nodes into sets such that parallel jobs will not be scheduled by Slurm across disjoint sets. Even though the topology.conf man-page refers to network switches, it’s really about topology rather than network. You may use fake (non-existing) switch names to describe the topology. For…

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In slurm; count number of folders in directory, encounter directory error

I have a lot of data to run through using slurm and I figured I could use a for loop sequence as it’s based on a range. The data takes a long time to generate so altering the output structure is not an option. The problem: When running my job…

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[slurm-users] Failed to forward X11 with a remote scheduler

Hi, I’m unsuccessful in running an X11 application with a remote SlurmctldHost. Let us call myfrontalnode the node from which the user is running the slurm commands that is different from the host SlurmctldHost. What fails is the following : ssh -X myfrontalnode srun –x11 xclock …

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Unable to download fastq files in parallel / SOS

Unable to download fastq files in parallel / SOS 0 Hi! Very new to all this so bear with me if I’m using incorrect terminology. Also english is my second language. I’m trying to download my fastq files in parallel but it doesn’t work and I keep receiving this error:…

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Computational Scientist-Bioinformatics in Chicago, IL for University of Chicago (UC)

  UPDATE: We are in process of fixing some issues with our job board search function. If you are experiencing any problems, we apologize for the inconvenience and thank you for your patience. Job Seekers, Welcome to HERC Jobs…

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POSTDOCTORAL FELLOW IN TRANSCRIPTOMICS AND BIOINFORMATICS

We are looking for an enthusiastic and ambitious postdoctoral fellow to study the pathophysiological bases of vascular anomalies via an integrated analysis of “omics” data (incl. single cell and bulk transcriptome, methylome, genome). The postdoctoral fellow will participate in all the omic aspects of the studies, from data analysis and…

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Phylogeographic reconstruction of the marbled crayfish origin

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

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Beagle 5.2 for imputation, outofmemory or ‘bus error’ any help?

Beagle 5.2 for imputation, outofmemory or ‘bus error’ any help? 0 Hi, I was trying to use beagle 5.2 for imputation of genotype data (N=62k). I was using chr21 with chunks of 3MB (total 12 chunks running in parallel). This tool is very fast. The problem is every time I…

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Average Amino Acid Identity (AAI) analysis manually

Average Amino Acid Identity (AAI) analysis manually 1 Hi all, I need to perform Average Amino Acid Identity (AAI) analysis for 422 genome using the SLURM system that only allows jobs to run for 3 days. Tool like compareM can’t finish the job on time. Therefore I wish to run…

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samtools server vs cluster error

Using inspiration from this thread HISAT2 output direct to bam, I’m attempting to run this command. The shell variables in this case represent paths to files/locations that make sense and in fact this command runs fine on my Ubuntu 18.04 LTS server using hisat 2.1 and samtools 1.10 (this seems…

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HPC Engineer at European Molecular Biology Laboratory (EMBL)

About the team/job We are seeking a HPC engineer to join our Compute team within our Technical Services Cluster (TSC), serving an institute of over 800 researchers and technical staff. You will be working closely with members of the department, and more widely with technical users across EMBL-EBI, playing an…

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MarkduplicatesSpark How to speed-up ?

MarkduplicatesSpark How to speed-up ? 0 Hello all, I would like to know if there is any good option to speed up MarkduplicatesSpark ? I work with human genome with arround 900 millions reads (151 bp). I work on a cluster (with slurm). The command that i used is (with…

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Senior Programmer Analyst/Bioinformatics in New York, NY for Columbia University

  Job Seekers, Welcome to HERC Jobs Senior Programmer Analyst/Bioinformatics Columbia University Columbia University Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range: Commensurate with experience  …

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IT System Engineer at European Molecular Biology Laboratory (EMBL)

About the team/job EMBL is Europe’s flagship research organization for the life sciences – an intergovernmental organization with more than 80 independent research groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its approx. 2000 employees of more than 80 nationalities, operate across six sites…

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