We have successfully installed (master-worker) nodes of cryosparc on HPC cluster,now we are facing issue to submit a job via pbs(job scheduler) on our HPC.We have followed all the steps as mentioned on guide CryoSPARC Installation Prerequisites - CryoSPARC Guide .
We are facing some challenges:
1.On our HPC system by default internet is not enabled, We have observed it verifies the license via your license server when we submit the job, it requires connectivity to cryosparc server.
Can we manage verification of license locally ?.
- We could run the job successfully using couple nodes as(worker nodes),now we need to integrate the cryosparc the pbs(job scheduler),So we are providing our cluster_script.sh. Please see the content of the cluster_script.sh as follows:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
#!/bin/sh
### Set the job name (for your reference)
#PBS -N cryosparc_{{ project_uid }}_{{ job_uid }}
### Set the project name, your department code by default
#PBS -P {{ project_uid }}
### Request email when job begins and ends
#PBS -m bea
### Specify email address to use for notification.
#PBS -M user_id
####
#PBS -l select=1:ncpus={{ num_cpu }}:ngpus={{ num_gpu }}
### Specify "wallclock time" required for this job, hhh:mm:ss
#PBS -l walltime=01:00:00
#PBS -o {{ job_log_path_abs }}
#PBS -e {{ job_log_path_abs }}
#PBS -l software=replace_with_Your_software_name
# After job starts, must goto working directory.
# $PBS_O_WORKDIR is the directory from where the job is fired.
echo "==============================="
echo $PBS_JOBID
cat $PBS_NODEFILE
echo "==============================="
cd $PBS_O_WORKDIR
#job
{{ run_cmd }} # Can you elaborate the {{run_cmd}}, it is calling which script or function?
+++++++++++++++++++++++++++++++++++++++++++++++++
- We are happy to share any other information with the cryosparc development team, regarding to our environment.
Our research work is totally stuck, we request your help in integrating cryosparc with pbs job scheduler.
We look forward your kind support as early as possible.
Looking for prompt response from cryosparc team.
Thanks,
Varun Jha
HPC Team,IITDelhi
