ABBYS HPC Module #slurm #sbatch


Kiran Das <s.kirandas@...>
 

Dear All,
I am facing problems with application modules in HPC.
Like the application works perfectly in master , but cannot run the same using sbatch or by interactive.
The error states that there is no modules found for the respective application. when in use 'module avail' there is no module available for respective application.
I create the module file using sample module file provided along with the Openhpc installation and loaded the module, but unfortunately that didn't worked.
If there is anybody using this application could help me to resolve this issue

Regards,
Kiran


jose_d
 

Hi,

could you pls share with us your module file, perhaps with sensitive information removed?

> Like the application works perfectly in master

have you installed the application on shared filesystem? If not, have you installed it on all nodes? Available in same path?
This sounds like something (paths, environment variables, etc..) is different there on computes..

cheers

Josef Dvoracek
On 02. 05. 19 6:52, Kiran Das wrote:

Dear All,
I am facing problems with application modules in HPC.
Like the application works perfectly in master , but cannot run the same using sbatch or by interactive.
The error states that there is no modules found for the respective application. when in use 'module avail' there is no module available for respective application.
I create the module file using sample module file provided along with the Openhpc installation and loaded the module, but unfortunately that didn't worked.
If there is anybody using this application could help me to resolve this issue

Regards,
Kiran


Karl W. Schulz
 

One other related comment: is the modulefile you created installed into the same path as other ohpc modules? If not, you may need to update the $MODULEPATH environment variable accordingly to include the path of your new modulefile.

-k

On May 2, 2019, at 4:33 AM, jose_d <jose@...> wrote:

Hi,

could you pls share with us your module file, perhaps with sensitive information removed?

> Like the application works perfectly in master

have you installed the application on shared filesystem? If not, have you installed it on all nodes? Available in same path?
This sounds like something (paths, environment variables, etc..) is different there on computes..

cheers

Josef Dvoracek
On 02. 05. 19 6:52, Kiran Das wrote:
Dear All,
I am facing problems with application modules in HPC.
Like the application works perfectly in master , but cannot run the same using sbatch or by interactive.
The error states that there is no modules found for the respective application. when in use 'module avail' there is no module available for respective application.
I create the module file using sample module file provided along with the Openhpc installation and loaded the module, but unfortunately that didn't worked.
If there is anybody using this application could help me to resolve this issue

Regards,
Kiran


Kiran Das <s.kirandas@...>
 

Dear All,

I tried with another application Blast as well but both are not working.

I could run this application in master and in individual nodes using ' source ~/.bash_profile'  , but cannot run using sbatch or srun

The application is available in master and nodes in the same path

Module file resides in the path "/opt/ohpc/pub/modulefiles/blast/"

The content of module file is as follows

#%Module1.0#####################################################################
proc ModulesHelp { } {​
    puts stderr " "​
    puts stderr "This module loads the blast program"​
    puts stderr "toolchain."​
    puts stderr "\nVersion 2.9\n"​
}​
module-whatis "Name: blast"​
module-whatis "Version: 2.9"​
module-whatis "Category: runtime library"​
module-whatis "Description: blast independant module"​
module-whatis "/"​
set     version                     1.0​
prepend-path    PATH                              /root/softwares/ncbi-blast-2.9.0+/bin​
prepend-path    MANPATH                    /root/softwares/ncbi-blast-2.9.0+​
prepend-path    INCLUDE                       /root/softwares/ncbi-blast-2.9.0+​
prepend-path    LD_LIBRARY_PATH     /root/softwares/ncbi-blast-2.9.0+​
setenv          BLAST_DIR          /root/softwares/ncbi-blast-2.9.0+​
setenv          BLAST_BIN          /root/softwares/ncbi-blast-2.9.0+/bin​
setenv          BLAST_LIB          /root/softwares/ncbi-blast-2.9.0+​
setenv          BLAST_INC          /root/softwares/ncbi-blast-2.9.0+

Please let me know if there is any changes required in module files 

Thanks & Regards,
Kiran


From: OpenHPC-users@groups.io <OpenHPC-users@groups.io> on behalf of Karl W. Schulz <karl@...>
Sent: Thursday, May 2, 2019 6:44 PM
To: OpenHPC-users@groups.io
Subject: Re: [openhpc-users] ABBYS HPC Module #slurm #sbatch
 
One other related comment: is the modulefile you created installed into the same path as other ohpc modules? If not, you may need to update the $MODULEPATH environment variable accordingly to include the path of your new modulefile.

-k

On May 2, 2019, at 4:33 AM, jose_d <jose@...> wrote:

Hi,

could you pls share with us your module file, perhaps with sensitive information removed?

> Like the application works perfectly in master

have you installed the application on shared filesystem? If not, have you installed it on all nodes? Available in same path?
This sounds like something (paths, environment variables, etc..) is different there on computes..

cheers

Josef Dvoracek
On 02. 05. 19 6:52, Kiran Das wrote:
Dear All,
I am facing problems with application modules in HPC.
Like the application works perfectly in master , but cannot run the same using sbatch or by interactive.
The error states that there is no modules found for the respective application. when in use 'module avail' there is no module available for respective application.
I create the module file using sample module file provided along with the Openhpc installation and loaded the module, but unfortunately that didn't worked.
If there is anybody using this application could help me to resolve this issue

Regards,
Kiran


John Hearns
 

I am a bit hesitant to say this, but there is a difference between interactive and non-interactive logins.
I have worked on this a lot in the past with Sun Gridengine.

You say:  I could run this application in master and in individual nodes using ' source ~/.bash_profile'  , but cannot run using sbatch or srun

I suggest that you put the relevant lines from your .bash_profile into your job script.




On Fri, 17 May 2019 at 10:50, Kiran Das <s.kirandas@...> wrote:
Dear All,

I tried with another application Blast as well but both are not working.

I could run this application in master and in individual nodes using ' source ~/.bash_profile'  , but cannot run using sbatch or srun

The application is available in master and nodes in the same path

Module file resides in the path "/opt/ohpc/pub/modulefiles/blast/"

The content of module file is as follows

#%Module1.0#####################################################################
proc ModulesHelp { } {​
    puts stderr " "​
    puts stderr "This module loads the blast program"​
    puts stderr "toolchain."​
    puts stderr "\nVersion 2.9\n"​
}​
module-whatis "Name: blast"​
module-whatis "Version: 2.9"​
module-whatis "Category: runtime library"​
module-whatis "Description: blast independant module"​
module-whatis "/"​
set     version                     1.0​
prepend-path    PATH                              /root/softwares/ncbi-blast-2.9.0+/bin​
prepend-path    MANPATH                    /root/softwares/ncbi-blast-2.9.0+​
prepend-path    INCLUDE                       /root/softwares/ncbi-blast-2.9.0+​
prepend-path    LD_LIBRARY_PATH     /root/softwares/ncbi-blast-2.9.0+​
setenv          BLAST_DIR          /root/softwares/ncbi-blast-2.9.0+​
setenv          BLAST_BIN          /root/softwares/ncbi-blast-2.9.0+/bin​
setenv          BLAST_LIB          /root/softwares/ncbi-blast-2.9.0+​
setenv          BLAST_INC          /root/softwares/ncbi-blast-2.9.0+

Please let me know if there is any changes required in module files 

Thanks & Regards,
Kiran


From: OpenHPC-users@groups.io <OpenHPC-users@groups.io> on behalf of Karl W. Schulz <karl@...>
Sent: Thursday, May 2, 2019 6:44 PM
To: OpenHPC-users@groups.io
Subject: Re: [openhpc-users] ABBYS HPC Module #slurm #sbatch
 
One other related comment: is the modulefile you created installed into the same path as other ohpc modules? If not, you may need to update the $MODULEPATH environment variable accordingly to include the path of your new modulefile.

-k

On May 2, 2019, at 4:33 AM, jose_d <jose@...> wrote:

Hi,

could you pls share with us your module file, perhaps with sensitive information removed?

> Like the application works perfectly in master

have you installed the application on shared filesystem? If not, have you installed it on all nodes? Available in same path?
This sounds like something (paths, environment variables, etc..) is different there on computes..

cheers

Josef Dvoracek
On 02. 05. 19 6:52, Kiran Das wrote:
Dear All,
I am facing problems with application modules in HPC.
Like the application works perfectly in master , but cannot run the same using sbatch or by interactive.
The error states that there is no modules found for the respective application. when in use 'module avail' there is no module available for respective application.
I create the module file using sample module file provided along with the Openhpc installation and loaded the module, but unfortunately that didn't worked.
If there is anybody using this application could help me to resolve this issue

Regards,
Kiran


Tru Huynh
 

Hi,

On Fri, May 17, 2019 at 09:50:00AM +0000, Kiran Das wrote:
...
#%Module1.0#####################################################################
prepend-path    PATH /root/softwares/ncbi-blast-2.9.0+/bin
...

Someone has installed everything under /root/softwares ???

/root is usually the $HOME for the root user.
it is local to every machine
it has restricted access (as every $HOME) and is probably not NFS shared
to all your compute nodes.

ymmv.

Tru

--
Tru Huynh (PhD) | mailto:tru@... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France