Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, That depends how your mpi is implemented, but what you really want is a filesystem visible on each node. But since mpirun gmx_mpi mdrun is working, then it's fine. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, I'm wondering, if I use gromacs in cluster environment, do I have to install gromacs in every nodes (at /usr/local/gromacs in every nodes) ? or is it enough to install gromacs in one node (example,in head-node) only ? Regards, Husen On Thu, Jun 23, 2016 at 3:41 PM, Mark Abraham

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, The only explanation is that that file is not in fact properly accessible if rank 0 is placed other than on "compute-node," which means your organization of file system / slurm / etc. aren't good enough for what you're doing. Mark On Thu, Jun 23, 2016 at 10:15 AM Husen R

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, I still unable to find out the cause of the fatal error. Previously, gromacs is installed in every nodes. That's the cause Build time mismatch and Build user mismatch appeared. Now, Build time mismatch and Build user mismatch issues are solved by installing Gromacs in shared directory. I

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, On Thu, Jun 16, 2016 at 12:24 PM Husen R wrote: > On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham > wrote: > > > Hi, > > > > There's just nothing special about any node at run time. > > > > Your script looks like it is building GROMACS fresh each

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

On Thu, Jun 16, 2016 at 4:01 PM, Mark Abraham wrote: > Hi, > > There's just nothing special about any node at run time. > > Your script looks like it is building GROMACS fresh each time - there's no > need to do that, which part of my script ? I always use this

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, There's just nothing special about any node at run time. Your script looks like it is building GROMACS fresh each time - there's no need to do that, but the fact that the node name is showing up in the check that takes place when the checkpoint is read is not relevant to the problem. Mark

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

On Thu, Jun 16, 2016 at 2:32 PM, Mark Abraham wrote: > Hi, > > On Thu, Jun 16, 2016 at 9:30 AM Husen R wrote: > > > Hi, > > > > Thank you for your reply ! > > > > md_test.xtc is exist and writable. > > > > OK, but it needs to be seen that way from the

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, On Thu, Jun 16, 2016 at 9:30 AM Husen R wrote: > Hi, > > Thank you for your reply ! > > md_test.xtc is exist and writable. > OK, but it needs to be seen that way from the set of compute nodes you are using, and organizing that is up to you and your job scheduler, etc. >

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, Thank you for your reply ! md_test.xtc is exist and writable. I tried to restart from checkpoint file by excluding other node than compute-node and it works. only '--exclude=compute-node' that produces this error. is this has the same issue with this thread ?

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi, The stuff about different nodes or numbers of nodes doesn't matter - it's merely an advisory note from mdrun. mdrun failed when it tried to operate upon md_test.xtc, so perhaps you need to consider whether the file exists, is writable, etc. Mark On Thu, Jun 16, 2016 at 6:48 AM Husen R

Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

this is the rest of the error message.. regards, Husen Halting parallel program gmx mdrun on rank 0 out of 16 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 Fatal error in PMPI_Bcast: Unknown error class, error stack: PMPI_Bcast(1635)..:

[gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi all, I got the following error message when I tried to restart gromacs simulation from checkpoint file. I restart the simulation using fewer nodes and processes, and also I exclude one node using '--exclude=' option (in slurm) for experimental purpose. I'm sure fewer nodes and processes are