Hello,
I am trying to compile/test Amber20 (tools + GPU-accelerated MD), on Summit at ORNL (IBM POWER9, NVIDIA V100s). The compile seems to run without a problem. When I `make test.serial`, most of the tests pass, but I see several errors similar to this one:
*/amber20/AmberTools/test/mdgx/1p7e$ ./Test.1p7e
ReadRst >> Attempted to read inpcrd as a NetCDF
ReadRst >> restart file, but failed.
grep: gb30.out: No such file or directory
grep: gb30.out: No such file or directory
grep: gb30.out: No such file or directory
diffing energy.dat.save with energy.dat
possible FAILURE: check energy.dat.dif
The part that is common to many of my errors is:
ReadRst >> Attempted to read inpcrd as a NetCDF
ReadRst >> restart file, but failed.
To try and resolve, I compiled allowing Amber to build NetCDF itself (rather than using the NetCDF provided by modules), but this did not help.
Does anyone have any thoughts as to why I would see multiple ReadRst/NetCDF errors? (or, if anyone has a cmake ‘recipe’ that works on Summit that would be awesome!)
When I run the compile/test, these are the modules I have loaded:
Currently Loaded Modules:
1) gcc/9.1.0
2) nsight-compute/2021.2.1
3) nsight-systems/2021.3.1.54
4) cuda/11.0.3
5) cmake/3.21.3
6) netlib-lapack/3.9.1
7) fftw/3.3.9
8) flex/2.6.4
9) bison/3.7.6
10) git/2.31.1
I’m using conda to manage python dependencies (I also tried letting Amber use miniconda, but this didn’t resolve the problem either).
Any assistance/advice here is greatly appreciated!
Thanks,
Derek
Derek M. Shore, Ph.D.
Scientific Computing Technology Engineer
Institute for Computational Biomedicine
Department of Physiology and Biophysics
Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room LC501A
New York, NY 10065
T: 212-746-6386
des2037.med.cornell.edu<mailto:
des2037.med.cornell.edu>
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Received on Fri Nov 19 2021 - 16:00:02 PST
