Dear Amber users
I have some possible failures and errors when I did "make test" for a
parallel (MPI) version of Amber18/AmberTools19.
I wonder if someone could let me what to do in order to solve this problem.
Here is a situation I have:
1. I installed a serial version of amber to a Linux workstation. It
seems that the installation was successfully completed, and I confirmed
that I did not have any possible failures and errors in the test for the
serial version.
2. I installed MPICH 3.3.2 to the workstation, following an instruction
of the reference manual of amber 2019 (p. 25).
3. I installed the parallel version of amber. It seems that the
installation was successfully completed. I defined "DO_PARALLEL" as
"mpirun -np 8" and did "make test". Then, I got some possible failures
and errors in this test.
I have attached log and diff files to this e-mail. I found that the
primary failures came from the test carried out in a directory of
phmd_remd/implicit.
However, I am not sure what to do to solve this problem...
I also did "make test" for different MPI libraries, such as MPICH 3.1.4,
OpenMPI 4.0.3, and OpenMPI 2.1.1.
Though calculated values were changed by using the different MPI
library, I still found the same possible failures and errors in the test
results.
The similar problem was reported by Zoran, which were posted to the
Amber Mailing List on February 5 2020.
(
http://archive.ambermd.org/202002/0055.html)
However, I could not find any answers for the problem in this post.
The specifications of the workstation I am using are shown below:
OS: CentOS 7.7.1908
Kernel: 3.10.0-1062.12.1.el7.x86_64
CPU: Intel Xeon Silver 4216 * 2
Memory: 96GB (16GB * 6)
It would be appreciated if you could let me know how to solve this problem.
Sincerely,
Kosuke Tachibana
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Received on Sun Mar 22 2020 - 21:30:02 PDT
