GROMACS version: 2018
GROMACS modification: Yes/No
I am trying to get the aggregation tendency of a polymer. In gromacs, I ran the following command. FYI, the top file has two polymer chains.
gmx_mpi clustsize -f …/polymer_agg.nojump.mol.xtc -n polymer.ndx -s polymer.tpr -mol yes -cut 0.35 -pbc yes
I got this error. What could be responsible for such an error? Kindly help!
Total number of atoms in clusters = 1
cmid: 1, cmax: 2, max_size: 2
50%^H^H^H^H100%^H^H^H^Hcmid: 2, cmax: 2, max_size: 2
Program: gmx clustsize, version 2018.1
Source file: src/gromacs/fileio/matio.cpp (line 681)
Fatal error:
Lo: 0.000000, Mid: 2.000000, Hi: 2.000000
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0)
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** STEP 13534.0 ON cpg029 CANCELLED AT 2020-04-14T16:26:38 ***
srun: error: cpg029: task 0: Exited with exit code 1