#!/bin/bash #SBATCH -p short #SBATCH -N 1 #SBATCH -n 20 #SBATCH [email protected],[email protected] #SBATCH --mail-type=ALL #SBATCH -t 1:0:00 #SBATCH -J A1002898126 #SBATCH -o /home/pga.submit/PGA_files/PROCESS_bc3d3c5f-30b9-48ab-bef7-e92fa8065f7a/MUSCLE.stdout #SBATCH -e /home/pga.submit/PGA_files/PROCESS_bc3d3c5f-30b9-48ab-bef7-e92fa8065f7a/MUSCLE.stderr
module load muscle cd /home/pga.submit/PGA_files/PROCESS_bc3d3c5f-30b9-48ab-bef7-e92fa8065f7a muscle -in inputFile -out outFile > On Jun 26, 2017, at 9:35 AM, Eroma Abeysinghe <[email protected]> > wrote: > > Hi Jarett, > > Did you do a recent upgrade of airavata and pga? If not please do so with the > latest production. By the information you have provided, it could be an issue > with gfac server reading from the rabbitmq queue. But you said although the > experiment is in LAUNCHED job is in submitted. So does your email contain > unread emails for this job? When was the last time the experiment completed > and any changes done to server machines, etc.. from then to now? > > Hi Jeff, > Yours is slightly different since its in EXECUTING. With the information you > have provided, I think your issue could be with email monitoring. Do you have > unread emails for the jobs in EXECUTING in your email box? If you do, then > you need to check you gfac-config.yaml in airavata bin folder and make sure > it processes emails from the comet. > > hope this info helps for further investigations. > > Thanks, > Eroma > > On Fri, Jun 23, 2017 at 4:56 PM, Sale, Jeff <[email protected] > <mailto:[email protected]>> wrote: > I have a similar issue. I have been working with the Airavata support folks, > Eroma, Supun, and Marcus for the past few weeks trying to get Gaussian jobs > to run on Comet. They have been super helpful, and it appears I am now able > to run jobs to completion according to the Gaussian.log file in the scratch > directory on Comet, but when I browse to the Experiment on the PGA the stdout > and stderr files never appear as a link in Outputs and the job status is > perpetually in "EXECUTING". > > I seem to recall Supun saying this was something they were aware of and are > working to resolve, but I could be wrong about this. > > Jeff > > ________________________________________ > From: Jarett DeAngelis [[email protected] <mailto:[email protected]>] > Sent: Friday, June 23, 2017 1:28 PM > To: [email protected] <mailto:[email protected]> > Subject: Job stuck in "launched," "submitted" status > > Hi gang, > > Working on our Airavata deployment (still build 16) again and have > encountered an issue where after submitting a job to Slurm, it gets stuck in > the “LAUNCHED” state, appearing to have sent the job to Slurm because it says > “SUBMITTED” underneath, but it just stays that way forever. If you look at > RabbitMQ there is a message sitting in the queue. Our first thought was that > it was the email account we’re using for job tracking, but that is > functioning fine. Where should I be looking for answers? > > Thanks, > Jarett > > > > -- > Thank You, > Best Regards, > Eroma
