Neuer Betreff: #BSUB -P abcd4321

25 Apr 2019

      Dear Subrata, dear all,
The error message is from slurm itself. For whatever reason, it doesn't
find the the slurm configuration file.
Which frontend (login) are you using?
For example on the login nodes you should be able to locate the file,
with all read flags set:
...
login18-1:~$ echo $HOSTNAME
login18-1.hpc.itc.rwth-aachen.de
login18-1:~$ locate slurm.conf
/etc/clustershell/groups.conf.d/slurm.conf.example
/etc/slurm/slurm.conf
/usr/share/doc/slurm-18.08.5-2/html/slurm.conf.html
/usr/share/man/man5/slurm.conf.5.gz
login18-1:~$ ls -lah /etc/slurm/slurm.conf
-r--r--r-- 1 root root 7.3K Apr 18 11:08 /etc/slurm/slurm.conf
On a different frontend, i.e. the copy server, you cannot:
...
copy:~$ echo $HOSTNAME
copy.hpc.itc.rwth-aachen.de
copy:~$ locate slurm.conf
/etc/clustershell/groups.conf.d/slurm.conf.example
/usr/share/doc/slurm-18.08.5-2/html/slurm.conf.html
/usr/share/man/man5/slurm.conf.5.gz
copy:~$ ls -lah /etc/slurm/slurm.conf
ls: cannot access /etc/slurm/slurm.conf: No such file or directory
Why sbatch is available on the node is a different question then:
...
copy:~$ command -v sbatch
/usr/bin/sbatch
On the old frontends the configuration file obviously doesn't exist
either, but sbatch still exists.
...
cluster:~$ echo $HOSTNAME
cluster.rz.RWTH-Aachen.DE
cluster:~$ locate slurm.conf
/etc/clustershell/groups.conf.d/slurm.conf.example
/usr/share/doc/slurm-18.08.5-2/html/slurm.conf.html
/usr/share/man/man5/slurm.conf.5.gz
cluster:~$ command -v sbatch
/usr/bin/sbatch
So make sure you login to one of the login nodes.
Best, Martin
Dr. Martin C. Schwarzer
RWTH Aachen University (Leitner Group, Hölscher Subgroup)
Worringerweg 2; 52074 Aachen; Germany
http://orcid.org/0000-0001-8435-9624
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On 2019-04-25 10:04, Subrata Pramanik wrote:
...
Dear All,
I am using Gromacs with following script:
#!/usr/bin/env zsh
#SBATCH -p c18m
#SBATCH --account=jara0187
#SBATCH -J Subrata1 
#SBATCH -o GROMACSJOB.o%J 
#SBATCH -e GROMACSJOB.e%J
#SBATCH --mail-user=s.pramanik@biotec.rwth-aachen.de
mailto:s.pramanik@biotec.rwth-aachen.de
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=end
#SBATCH -n 24
#SBATCH --mem-per-cpu=5000
#SBATCH -t 24:00:00

###### end of Slurm  directives ######
###### start of shell commands ######
### load the necessary module files
module load CHEMISTRY
module load gromacs/5.1.2
#path for job file
cd $HOME/run1-test
# Start the MPI-parallel mdrun directly ...
$SLURM_NTASKS gmx_mpi mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
I am getting this error: 
sbatch: error: s_p_parse_file: unable to status file
/etc/slurm/slurm.conf: No such file or directory, retrying in 1sec up to
60sec
sbatch: error: ClusterName needs to be specified
sbatch: fatal: Unable to process configuration file
If anybody has any suggestions, please let me know.
Thanks in advance.
Best regards,
Subrata
On Thu, Apr 25, 2019 at 9:57 AM Julien Guénolé
<guenole@imm.rwth-aachen.de mailto:guenole@imm.rwth-aachen.de> wrote:
Thanks to answer to the list: it can always be helpful to others...

If you get an error with these,

#SBATCH -p c18m
#SBATCH --account=jara0187

I don't know what to suggest more.

Best wishes,
Julien

On 25/04/2019 09:20, Subrata Pramanik wrote:

...
Dear Julien,

Thank you for your suggestion.

In the LSF, I had this way: 

##BSUB -P rwth0031
#BSUB -P jara0187

In the SLURM, I changed in these ways: 

#SBATCH -p c18m
#SBATCH --account=jara0187

OR

#SBATCH -p rwth0031
#SBATCH --account=jara0187

In both cases, I am getting the same error: 
sbatch: error: s_p_parse_file: unable to status file
/etc/slurm/slurm.conf: No such file or directory, retrying in 1sec
up to 60sec
sbatch: error: ClusterName needs to be specified
sbatch: fatal: Unable to process configuration file

I am herewith sending the script file. If possible, please have a
look and suggest me.

Thanks in advance.

Best regards,
Subrata. 

On Wed, Apr 24, 2019 at 5:36 PM Julien Guénolé
<guenole@imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de>>
wrote:

    As indicated by the error message, did you try to specify the
    ClusterName? For example:

    #SBATCH -p c18m

    if there is still an error, a copy of the batch file could be
    useful!

    Best wishes,
    Julien

    On 24/04/2019 17:27, Subrata Pramanik wrote:

...
    Hi all,

    I am trying to submit a job to Gromacs using cluster.

    With LSF, it was working well. 

    I am getting the follwong error: 

    sbatch: error: s_p_parse_file: unable to status file
    /etc/slurm/slurm.conf: No such file or directory, retrying in
    1sec up to 60sec
    sbatch: error: ClusterName needs to be specified
    sbatch: fatal: Unable to process configuration file

    Please suggest me to solve this problem.

    Thanks in advance.

    Best regards,
    Subrata.

    On Tue, Mar 12, 2019 at 8:20 PM Philipp Rüßmann
    <p.ruessmann@fz-juelich.de
    <mailto:p.ruessmann@fz-juelich.de>> wrote:

        Dear Marek,

        the command is #SBATCH --account=abcd1234.

        Cheers,
        Philipp

        Am 12.03.19 um 20:01 schrieb simon@isf.rwth-aachen.de
        <mailto:simon@isf.rwth-aachen.de>:
        > Hi all,
        >
        > Is there an equivalent of the #BSUB -p command in SLURM
        as well?
        >
        > Best Wishes,
        > Marek
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    -- 
    Yours Sincerely,

    Subrata Pramanik

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-- 
Yours Sincerely,

Subrata Pramanik

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**************************************************
Dr. Julien GUÉNOLÉ
Research Group Head
----------------------
Institute of Physical Metallurgy and Metal Physics
RWTH Aachen University
Kopernikusstrasse 14
52074 Aachen, GERMANY
---------------------- Room 202
Phone [office] +49 241 80 26866
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Yours Sincerely,
Subrata Pramanik

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Re: #BSUB -P abcd4321