Dear Amber users,
I did installation of both serial and parallel version of Amber18 without
any error. Serial test passed with 0 error. However, when ran the parallel
test I got an error saying "Could not import Amber Python modules!".
In my knowledge I correctly set the path for Python still getting the same
problem. I did the configuration in the following way.
./configure --with-python
/home/external/cbs/sunitap/softwares/Python-3.6.0/bin/python -mpi gnu
Please help me where I am going wrong. Pls see the excerpts pasted below.
I searched the mailing list and tried all the possible suggestions. Still
getting the same problem.
System was having older python 2.6 so installed Phython3.6 locally and set
path.
echo $PYTHONPATH
/home/external/cbs/sunitap/softwares/amber18/lib/python3.6/site-packages
Thanks in advance.
Sunita
--------------- .bashrc setting for Amber installation----------------
export AMBERHOME=/home/external/cbs/sunitap/softwares/amber18
source /home/external/cbs/sunitap/softwares/amber18/amber.sh
alias python=/home/external/cbs/sunitap/softwares/Python-3.6.0/bin/python
---------------Parallel installation---------------
make[3]: Leaving directory
`/home/external/cbs/sunitap/softwares/amber18/src/pmemd/src'
Installation of pmemd.MPI complete
make[2]: Leaving directory
`/home/external/cbs/sunitap/softwares/amber18/src/pmemd'
Installation of Amber18 (parallel) is complete at Mon Aug 19 18:12:27 IST
2019.
make[1]: Leaving directory
`/home/external/cbs/sunitap/softwares/amber18/src'
------------------Serial test----------------
Finished serial test suite for Amber 18 at Mon Aug 19 15:20:00 IST 2019.
178 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as
/home/external/cbs/sunitap/softwares/amber18/logs/test_amber_serial/2019-08-19_14-51-44.log
No test diffs to save!
================Parallel test===========
export DO_PARALLEL="mpirun -np 2"
[sunitap.ycn2 amber18]$ make test
(cd AmberTools/test && make test.parallel)
make[1]: Entering directory
`/home/external/cbs/sunitap/softwares/amber18/AmberTools/test'
./test_at_parallel.sh
Tests being run with DO_PARALLEL="mpirun -np 2".
*Error:* Could not import Amber Python modules!
Probably your Amber Python environment was not set up correctly.
We recommend adding the line:
test -f /home/external/cbs/sunitap/softwares/amber18/amber.sh && source
/home/external/cbs/sunitap/softwares/amber18/amber.sh (sh/bash/zsh)
or
test -f /home/external/cbs/sunitap/softwares/amber18/amber.csh && source
/home/external/cbs/sunitap/softwares/amber18/amber.csh (csh/tcsh)
to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc).
make[1]: *** [test.parallel] *Error 1*
make[1]: Leaving directory
`/home/external/cbs/sunitap/softwares/amber18/AmberTools/test'
make: *** [test.parallel] *Error 2*
================
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Received on Mon Aug 19 2019 - 23:00:02 PDT
