dhdegroot
commented
2 years ago Hi, @EBaalhuis agreed to look into this. He will contact you shortly.
Closed ylwed closed 1 year ago
dhdegroot
commented
2 years ago Hi, @EBaalhuis agreed to look into this. He will contact you shortly.
EBaalhuis
commented
2 years ago Hi @ylwed can you send me the singularity definition file, the SLURM script and the log-files?
ylwed
commented
2 years ago Hello!
Here are the files. Also, we have now managed to run the program on the HPC environment at my campus! The program at our campus uses CPLEX as the linear solver and not GLPK, so we have not yet figured out the mystery of GLPK.
We managed to run ecmtool by downloading all dependencies locally. Unfortunately I do not know exactly how these dependencies were downloaded and installed, as the local IT-support helped me with this. Therefore it would be ideal to create a container with the right dependencies, so I still appreaciate help with this.
Thank you for looking into this!
Regards, Ylva Wedmark
Fra: Erik @.> Sendt: mandag 28. februar 2022 kl. 18.17 Til: @.> Kopi: @.>; @.> Emne: Re: [SystemsBioinformatics/ecmtool] GLPK is not recognized (Issue #14)
Hi @ylwedhttps://github.com/ylwed can you send me the singularity definition file, the SLURM script and the log-files?
— Reply to this email directly, view it on GitHubhttps://github.com/SystemsBioinformatics/ecmtool/issues/14#issuecomment-1054480964, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AX5EVPZE475VYESAI3VIPALU5OU3LANCNFSM5PEODYVA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>
tjclement
commented
2 years ago Update on this: Ylva has ecmtool running in singularity, but there appears to be a crash during the compression phase. She'll send over the singularity config to me, and I'll then test it locally to see what might be going on.
ylwed
commented
2 years ago Hello, Tom!
Thank you so much for the talk yesterday! I have attached the singularity definition file in this mail, so you are free to look into it!
Regards, Ylva
Fra: Tom @.> Sendt: fredag 8. april 2022 kl. 17.21 Til: @.> Kopi: @.>; @.> Emne: Re: [SystemsBioinformatics/ecmtool] GLPK is not recognized (Issue #14)
Update on this: Ylva has ecmtool running in singularity, but there appears to be a crash during the compression phase. She'll send over the singularity config to me, and I'll then test it locally to see what might be going on.
— Reply to this email directly, view it on GitHubhttps://github.com/SystemsBioinformatics/ecmtool/issues/14#issuecomment-1092996919, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AX5EVPZ3LRQTIYF7WCFUBZLVEBFF5ANCNFSM5PEODYVA. You are receiving this because you were mentioned.Message ID: @.***>
Hello!
I'm trying to install ecmtool on a HPC environment on my campus in a singularity container. So far, I'm having a problem with the GLPK solver: Even though GLPK is installed and loaded in the environment, the program states that it is not available. I'm not sure whether the problem is the installation or loading of the GLPK solver or if it is a problem with ecmtool. It does seem ecmtool is able to use CPLEX, but only the python interface is installed in the environment, so it is likely not actually used.
If anyone would like to look into this, I would be happy to send the singularity definition file, the SLURM script and the log-files.