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Jerkwin / gmxtools

tools for GROMACS
https://jerkwin.github.io/gmxtools/
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trr2all: Can't recognize gmx dump with trr2all Tool on Linux Cluster #9

Closed unknown-fractal closed 6 months ago

unknown-fractal commented 7 months ago

Dear Dr. Li,

I encountered some issues while using your trr2all tool. Due to the significant computational load, I attempted to utilize the tool on a Linux cluster. It seems that I managed to run the .exe file using Wine, yet encountered errors during execution, as follows:

Can't recognize 'gmx_mpi dump -s /home/aczzq/ach-test.tpr -quiet ' as an internal or external command, or batch script.
At line 95 of file G:\Dropbox\prog\trr2all\trr2all.f90 (unit = 100, file = '/home/aczzq/ach-test.dmp')
Fortran runtime error: End of file

Error termination. Backtrace:

Could not print backtrace: executable file is not COFF
#0  0xffffffff
#1  0xffffffff
#2  0xffffffff
#3  0xffffffff
#4  0xffffffff
#5  0xffffffff
#6  0xffffffff
#7  0xffffffff
#8  0xffffffff
#9  0xffffffff
#10  0xffffffff
#11  0xffffffff
#12  0xffffffff
#13  0xffffffff
#14  0xffffffff
#15  0xffffffff
#16  0xffffffff

Given that your tool is compiled in .exe format, I find it challenging to pinpoint the source of the problem. I attempted to run the problematic command (gmx_mpi dump -s /home/aczzq/ach-test.tpr -quiet) in the terminal, and it executed without errors. Hence, I am uncertain about resolving this issue and would greatly appreciate your assistance amidst your busy schedule.

Thank you very much.

Jerkwin commented 6 months ago

Hi,

Sorry for the delay reply since I was on vacation last week.

For the issue, I would suggest trying using full path of gmx for -gmx option. If it still fails, please let me know through my Gmail and I will send you the source code so that you can compile it on Linux.

Jicun

unknown-fractal commented 6 months ago

Hi,

Sorry for the delay reply since I was on vacation last week.

For the issue, I would suggest trying using full path of gmx for -gmx option. If it still fails, please let me know through my Gmail and I will send you the source code so that you can compile it on Linux.

Jicun

Dear Dr. Li, Thank you very much for your response. It seems that my issue did indeed occur for this reason. Unfortunately, due to the urgency of my work, I had already carried out a similar operation through other means, and therefore was unable to reply promptly. Nevertheless, I appreciate your solution.