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 E-mails sent by me are always PGP/MIME signed. If you are unable to open attachments because of this, you might be using an outdated e-mail client. In this case, please contact me and I will send you the message with PGP/inline instead. 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 > _______________________________________________ > claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> > To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>
-- Dr. rer. nat. Philipp Rüßmann Peter Grünberg Institut (PGI-1) and Institute for Advanced Simulation (IAS-1) Forschungszentrum Jülich GmbH, D-52425 Jülich Tel.: +49 2461 61-5523 E-Mail: p.ruessmann@fz-juelich.de <mailto:p.ruessmann@fz-juelich.de>
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>
-- Yours Sincerely,
Subrata Pramanik
_______________________________________________ claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>
-- ************************************************** 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 Email guenole@imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de> Web http://www.julien-guenole.fr Twitter @nanouayeur **************************************************
_______________________________________________ claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>
-- Yours Sincerely,
Subrata Pramanik
-- ************************************************** 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 Email guenole@imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de> Web http://www.julien-guenole.fr Twitter @nanouayeur **************************************************
_______________________________________________ claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>
-- Yours Sincerely,
Subrata Pramanik
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Dear Martin, Dear Sebastian, Dear Simon, Dear All, Thank you for your suggestion. I used claix 18 login nodes: login18-1.hpc.itc.rwth-aachen.de It is possible to submit a job now. I am getting an error with Project name. I am using a project "jara0187" for computer time as following #SBATCH -p c18m #SBATCH --account=jara0187 It is telling: Given account jara0187 not found in config. Without #SBATCH --account=jara0187, I could submit. However, the job is getting exit by the following: Job ID: 1488261 Cluster: rcc User/Group: rs797177/rs797177 State: FAILED (exit code 127) Nodes: 2 Cores per node: 12 CPU Utilized: 00:00:00 CPU Efficiency: 0.00% of 00:06:00 core-walltime Job Wall-clock time: 00:00:15 Memory Utilized: 0.00 MB (estimated maximum) Memory Efficiency: 0.00% of 117.19 GB (4.88 GB/core) Thank you. Best regards, Subrata On Thu, Apr 25, 2019 at 10:58 AM Martin C. Schwarzer <schwarzer@mail.de> wrote:
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
E-mails sent by me are always PGP/MIME signed. If you are unable to open attachments because of this, you might be using an outdated e-mail client. In this case, please contact me and I will send you the message with PGP/inline instead.
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 > _______________________________________________ > claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> > To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>
-- Dr. rer. nat. Philipp Rüßmann Peter Grünberg Institut (PGI-1) and Institute for Advanced Simulation (IAS-1) Forschungszentrum Jülich GmbH, D-52425 Jülich Tel.: +49 2461 61-5523 E-Mail: p.ruessmann@fz-juelich.de <mailto:p.ruessmann@fz-juelich.de>
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
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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 Email guenole@imm.rwth-aachen.de <mailto: guenole@imm.rwth-aachen.de> Web http://www.julien-guenole.fr Twitter @nanouayeur **************************************************
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-- Yours Sincerely,
Subrata Pramanik
-- ************************************************** 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 Email guenole@imm.rwth-aachen.de <mailto: guenole@imm.rwth-aachen.de> Web http://www.julien-guenole.fr Twitter @nanouayeur **************************************************
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-- Yours Sincerely,
Subrata Pramanik
_______________________________________________ claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de
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-- Yours Sincerely, Subrata Pramanik
Dear All, I have same problem... best Alexey Sorokin Lehrstuhl für Experimentelle Molekulare Bildgebung (ExMI) Universitätsklinikum Aachen Pauwelsstrasse 30, D-52074 Aachen Tel.: +49 (0)08448975 http://exmi.rwth-aachen.de<https://ex-mailbox.klinikum.rwth-aachen.de/OWA/redir.aspx?C=v6gerjCg0hCvQ-U-lLsTVZQpZwFCn9K1LMx8ZjEHi-VrvJ6O5-DVCA..&URL=http%3a%2f%2fexmi.rwth-aachen.de%2f> ________________________________ От: Subrata Pramanik <subrata.biocell@gmail.com> Отправлено: 25 апреля 2019 г. 11:17 Кому: Martin C. Schwarzer Копия: claix18-slurm-pilot@lists.rwth-aachen.de Тема: [claix18-slurm-pilot] Re: #BSUB -P abcd4321 Dear Martin, Dear Sebastian, Dear Simon, Dear All, Thank you for your suggestion. I used claix 18 login nodes: login18-1.hpc.itc.rwth-aachen.de<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flogin18-1.hpc.itc.rwth-aachen.de%2F&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269322742&sdata=iShNQ7QB%2FlQYENc7YfBhOalZQXMAZ9f7WYJ%2BbyiRtM4%3D&reserved=0> It is possible to submit a job now. I am getting an error with Project name. I am using a project "jara0187" for computer time as following #SBATCH -p c18m #SBATCH --account=jara0187 It is telling: Given account jara0187 not found in config. Without #SBATCH --account=jara0187, I could submit. However, the job is getting exit by the following: Job ID: 1488261 Cluster: rcc User/Group: rs797177/rs797177 State: FAILED (exit code 127) Nodes: 2 Cores per node: 12 CPU Utilized: 00:00:00 CPU Efficiency: 0.00% of 00:06:00 core-walltime Job Wall-clock time: 00:00:15 Memory Utilized: 0.00 MB (estimated maximum) Memory Efficiency: 0.00% of 117.19 GB (4.88 GB/core) Thank you. Best regards, Subrata On Thu, Apr 25, 2019 at 10:58 AM Martin C. Schwarzer <schwarzer@mail.de<mailto:schwarzer@mail.de>> wrote: 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 $HOSTNAME login18-1.hpc.itc.rwth-aachen.de<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flogin18-1.hpc.itc.rwth-aachen.de&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269322742&sdata=6f5MqlzYqrkXSdsc3gPh460Aa9W5pojjySSvSqXsjKY%3D&reserved=0> login18-1:~$ 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 $HOSTNAME copy.hpc.itc.rwth-aachen.de<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcopy.hpc.itc.rwth-aachen.de&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269332752&sdata=l5zgCzILnpxJ%2BAycNqH1CLHjorPUOILz7oRVuETKe0c%3D&reserved=0> copy:~$ 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 $HOSTNAME cluster.rz.RWTH-Aachen.DE<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcluster.rz.RWTH-Aachen.DE&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269332752&sdata=UcyVkVx5z%2FPx%2ByckSsWGpHCqh6TQEtds%2FxFEr7%2FJBLM%3D&reserved=0> cluster:~$ 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<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F0000-0001-8435-9624&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269342757&sdata=8c%2BdvSDsild8h%2FIP%2BNUJTUIRLFmiDdLxtb6f8OQfGTw%3D&reserved=0> E-mails sent by me are always PGP/MIME signed. If you are unable to open attachments because of this, you might be using an outdated e-mail client. In this case, please contact me and I will send you the message with PGP/inline instead. 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> <mailto: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> <mailto: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> <mailto: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> <mailto: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> <mailto: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 > _______________________________________________ > claix18-slurm-pilot mailing list -- claix18-slurm-pilot@lists.rwth-aachen.de<mailto:claix18-slurm-pilot@lists.rwth-aachen.de> <mailto:claix18-slurm-pilot@lists.rwth-aachen.de<mailto:claix18-slurm-pilot@lists.rwth-aachen.de>> > To unsubscribe send an email to claix18-slurm-pilot-leave@lists.rwth-aachen.de<mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de<mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de>>
-- Dr. rer. nat. Philipp Rüßmann Peter Grünberg Institut (PGI-1) and Institute for Advanced Simulation (IAS-1) Forschungszentrum Jülich GmbH, D-52425 Jülich Tel.: +49 2461 61-5523 E-Mail: p.ruessmann@fz-juelich.de<mailto:p.ruessmann@fz-juelich.de> <mailto:p.ruessmann@fz-juelich.de<mailto:p.ruessmann@fz-juelich.de>>
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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 Email guenole@imm.rwth-aachen.de<mailto:guenole@imm.rwth-aachen.de> <mailto:guenole@imm.rwth-aachen.de<mailto:guenole@imm.rwth-aachen.de>> Web http://www.julien-guenole.fr<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.julien-guenole.fr&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269342757&sdata=NUn%2Fpha1wRR3J%2Bsobz3MVli8zgSBES9EF3oZT1PJsVw%3D&reserved=0> Twitter @nanouayeur **************************************************
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-- Yours Sincerely,
Subrata Pramanik
-- ************************************************** 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 Email guenole@imm.rwth-aachen.de<mailto:guenole@imm.rwth-aachen.de> <mailto:guenole@imm.rwth-aachen.de<mailto:guenole@imm.rwth-aachen.de>> Web http://www.julien-guenole.fr<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.julien-guenole.fr&data=02%7C01%7C%7Cd68201a6e8dc4ab2c3c808d6c95f3fe1%7C5a6d5ee56edf4a26ba93f5872dbb9614%7C0%7C0%7C636917808269352767&sdata=dVY%2BNIDGB8UmEWhP%2BwHg45rUPpTdLzIrzJ4B9khDM1g%3D&reserved=0> Twitter @nanouayeur **************************************************
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-- Yours Sincerely,
Subrata Pramanik
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participants (4)
-
Martin C. Schwarzer -
Sascha Buecken -
Sorokin, Alexey -
Subrata Pramanik