Added Known Problems and Troubleshooting (splitted)
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@ -15,8 +15,6 @@ entries:
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url: /merlin6/code-of-conduct.html
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- title: Hardware And Software Description
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url: /merlin6/hardware-and-software.html
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- title: Migrating From Merlin5
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url: /merlin6/migrating.html
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- title: Accessing Merlin
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folderitems:
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- title: Requesting Accounts
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@ -39,7 +37,11 @@ entries:
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url: /merlin6/running-jobs.html
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- title: Support
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folderitems:
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- title: Migrating From Merlin5
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url: /merlin6/migrating.html
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- title: Known Problems
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url: /merlin6/known-problems.html
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- title: Troubleshooting
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url: /merlin6/troubleshooting.html
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- title: Contact
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url: /merlin6/contact.html
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- title: Known Problems and Troubleshooting
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url: /merlin6/troubleshooting.html
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@ -1,83 +0,0 @@
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---
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title: Known Problems and Troubleshooting
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#tags:
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#keywords:
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last_updated: 13 June 2019
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#summary: ""
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sidebar: merlin6_sidebar
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permalink: /merlin6/troubleshooting.html
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---
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## Known Problems
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### Paraview, ANSYS and OpenGL
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Try to use X11(mesa) driver for Paraview and ANSYS instead of OpenGL:
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```bash
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# ANSYS
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module load ANSYS
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fluent -driver x11
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# ParaView
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module load paraview
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paraview --mesa
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```
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###+ Illegal instructions
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It may happened that your code, compiled on one machine will not be executed on another throwing exception like "(Illegal instruction)".
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Check (with "hostname" command) on which of the node you are and compare it with the names from first item. We observe few applications
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that can't be run on merlin-c-01..16 because of this problem (notice that these machines are more then 5 years old). Hint: you may
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choose the particular flavour of the machines for your slurm job, check the "--cores-per-node" option for sbatch:
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```bash
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sbatch --cores-per-socket=8 Script.sh # will filter the selection of the machine and exclude the oldest one, merlin-c-01..16
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```
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## Troubleshooting
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### Before asking for help
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Please, if you have problems running jobs and you want to report something or just ask for help,
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please gather and attach in advance the following information:
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* Unix username and session (``who am i`` command output)
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* Environment settings (``env`` command output)
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* Slurm batch script location (path to script and input/output files)
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* Slurm job_id (``id`` is returned on ``sbatch``/``salloc`` command, but also can be taken from ``squeue`` commmand)
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### Troubleshooting SSH
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Use the ssh command with the "-vvv" option and copy and paste (no screenshot please)
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the output to your request in Service-Now. Example
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```bash
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ssh -Y -vvv bond_j@merlin-l-01
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```
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### Troubleshooting SLURM
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If one copies Slurm commands or batch scripts from another cluster,
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they may need some changes (often minor) to run successfully on Merlin5.
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Examine carefully the error message, especially concerning the options
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used in the slurm commands.
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Try to submit jobs using the examples given in the section "Using Batch System to Submit Jobs to Merlin5".
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If you can run successfully an example for a type of job (!OpenMP, MPI) similar to your one,
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try to edit the example to run your application.
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If the problem remains, then, in your request in Service-Now, describe the problem in details that
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are needed to reproduce it. Include the output of the following commands:
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```bash
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date
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hostname
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pwd
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module list
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# All slurm commands used with the corresponding output
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```
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Do not delete any output and error files generated by Slurm.
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Make a copy of the failed job script if you like to edit it meanwhile.
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36
pages/merlin6/known-problems.md
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36
pages/merlin6/known-problems.md
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@ -0,0 +1,36 @@
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---
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title: Known Problems
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#tags:
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#keywords:
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last_updated: 20 June 2019
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#summary: ""
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sidebar: merlin6_sidebar
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permalink: /merlin6/known-problems.html
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---
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## Known Problems
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### Paraview, ANSYS and OpenGL
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Try to use X11(mesa) driver for Paraview and ANSYS instead of OpenGL:
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```bash
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# ANSYS
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module load ANSYS
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fluent -driver x11
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# ParaView
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module load paraview
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paraview --mesa
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```
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###+ Illegal instructions
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It may happened that your code, compiled on one machine will not be executed on another throwing exception like "(Illegal instruction)".
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Check (with "hostname" command) on which of the node you are and compare it with the names from first item. We observe few applications
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that can't be run on merlin-c-01..16 because of this problem (notice that these machines are more then 5 years old). Hint: you may
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choose the particular flavour of the machines for your slurm job, check the "--cores-per-node" option for sbatch:
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```bash
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sbatch --cores-per-socket=8 Script.sh # will filter the selection of the machine and exclude the oldest one, merlin-c-01..16
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```
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43
pages/merlin6/troubleshooting.md
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43
pages/merlin6/troubleshooting.md
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@ -0,0 +1,43 @@
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---
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title: Troubleshooting
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#tags:
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#keywords:
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last_updated: 20 June 2019
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#summary: ""
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sidebar: merlin6_sidebar
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permalink: /merlin6/troubleshooting.html
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---
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For troubleshooting, please contact us through the official channels. See [Contact](/merlin6/contact.html)
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for more information.
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## Troubleshooting running Slurm jobs
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If you want to report a problem or request for help when running jobs, please **always provide**
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the following information:
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1. Provide your batch script or, alternatively, the path to your batch script.
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2. Add **always** the following commands to your batch script
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```bash
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echo "User information:"; who am i
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echo "Running hostname:"; hostname
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echo "Current location:"; pwd
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echo "User environment:"; env
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echo "List of PModules:"; module list
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```
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3. Whenever possible, provide the Slurm JobID.
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Providing this information is **extremely important** in order to ease debugging, otherwise
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only with the description of the issue or just the error message is completely insufficient
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in most cases.
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### Troubleshooting SSH
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Use the ssh command with the "-vvv" option and copy and paste (no screenshots please)
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the output to your request in Service-Now. Example
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```bash
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ssh -Y -vvv $username@merlin-l-01.psi.ch
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```
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