So, this time around the serial configuration and compilation proceeded with some warnings though without errors. The tests did, however, report possible errors/failures that in part seems to stem from some python (or just pytraj) issue.
The parallell installation using external and global openMPI version 4.0.1. also proceeded with some warnings though without errors. Once more the -openmp configuration for cpptraj parallell NetCDF support failed with an incompatibility issue.
Attached are the registered potential failures/errors for the clang serial installation. Running the parallell tests is not possible in the current manner as every test generates a “Allow incoming network connection” popup and turning the firewall off just produces a direct failure for all tests.
### INSTALLATION ###
# As I have already done this, I cannot comment on the step being needed or not
$ open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
$ export AMBERHOME=/Users/guolaa/SOFTWARE/amber18
$ export PATH=${AMBERHOME}:$PATH
$ export MACOSX_DEPLOYMENT_TARGET='10.14'
$ ./configure -macAccelerate clang
$ make install
Installation complete
$ ./configure -macAccelerate -mpi clang
$ make install
Installation complete
$ export DO_PARALLEL="mpirun -np 4"
make test
—> First firewall issues, turning off the firewall produces the following:
Finished test suite for AmberTools at Sat Apr 27 09:22:45 CEST 2019.
3 file comparisons passed
693 file comparisons failed ( 0 ignored)
689 tests experienced errors
Test log file saved as /amber18/logs/test_at_parallel/2019-04-27_09-21-56.log
Test diffs file saved as /amber18/logs/test_at_parallel/2019-04-27_09-21-56.diff
make[1]: *** [test.parallel] Error 1
make: [test.parallel] Error 2 (ignored)
./configure -macAccelerate -openmp clang
Using the AmberTools miniconda installation in /Users/guolaa/SOFTWARE/amber18/miniconda
version 2.7.15
OpenMP and clang are not currently compatible
Configure failed due to the errors above!
#### POTENTIAL SERIAL TEST ISSUES ###
********************************************************************************
TEST: /amber18/AmberTools/src/cpptraj/test/Test_XtalSymm
==============================================================
cd pytraj && /Applications/Xcode.app/Contents/Developer/usr/bin/make
Testing serial pytraj
/amber18/bin/amber.python test.py
Traceback (most recent call last):
File "test.py", line 2, in <module>
import pytraj as pt
ImportError: No module named pytraj
test.pytraj: Program error
============================= test session starts ==============================
platform darwin -- Python 2.7.15, pytest-4.4.1, py-1.8.0, pluggy-0.9.0 -- /amber18/bin/amber.python
cachedir: .pytest_cache
rootdir: /amber18/AmberTools/src/pytraj
collecting ... collected 0 items / 1 errors
==================================== ERRORS ====================================
__________ ERROR collecting tests/test_energy/test_sander_energies.py __________
ImportError while importing test module '/amber18/AmberTools/src/pytraj/tests/test_energy/test_sander_energies.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../miniconda/lib/python2.7/site-packages/six.py:709: in exec_
exec("""exec _code_ in _globs_, _locs_""")
../../src/pytraj/tests/test_energy/test_sander_energies.py:4: in <module>
import pytraj as pt
E ImportError: No module named pytraj
!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!
=========================== 1 error in 0.20 seconds ============================
--> So it seems that the pytraj module was not correctly installed.
==============================================================
cd ../src/FEW/examples/test && AMBER_SOURCE=/amber18 ./Run.few.test
#########################################################################
PERFORMING FEW TESTS
If all of the tests below fail then check the system specific path to
the locally installed Perl libraries.
For details on test issues and on how to fix them read:
/amber18/AmberTools/src/FEW/examples/test/few.log
CLEANING
PERFORMING TEST 01: Step1 of RESP charge calculation
CHECKING IN TEST 01: Step1 of RESP charge calculation
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/gauss/L51a/L51a.gcrt does not exist.
==============================================================
mv: rename /amber18/AmberTools/src/FEW/examples/test/gauss to /amber18/AmberTools/src/FEW/examples/test/gauss_setup: No such file or directory
PERFORMING TEST 02: Step2 of RESP charge calculation and setup of MD simulations
CHECKING IN TEST 02: Step2 of RESP charge calculation and setup of MD simulations
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/gauss/L51a/L51a.gout.xyz does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/leap/L51a/L51a_resp.lib does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/leap/L51a/L51a.frcmod does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/leap/L51a/L51a_com.pdb does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/leap/L51a/L51a_rec.pdb does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/leap/L51a/L51a_lig.pdb does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_com.crd does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_rec.crd does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_lig.crd does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/equi/md_nvt_red_06.in does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/rec/equi/md_nvt_red_06.in does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/prod/md_prod_001.in does not exist.
==============================================================
possible FAILURE: file /amber18/AmberTools/src/FEW/examples/test/MD_resp/rec/prod/md_prod_001.in does not exist.
==============================================================
--> Don't exactly know what happened though something is apparently missing.
==============================================================
Testing the Python LES API
/amber18/bin/amber.python test.py
Could not import sanderles. Skipping test
--> Seems like there is an issue with python
Finished test suite for AmberTools at Sat Apr 27 08:27:19 CEST 2019.
2077 file comparisons passed
16 file comparisons failed ( 1 ignored)
20 tests experienced errors
Test log file saved as /amber18/logs/test_at_serial/2019-04-27_07-40-53.log
Test diffs file saved as /amber18/logs/test_at_serial/2019-04-27_07-40-53.diff
--- DIFFS ---
possible FAILURE: check addles.out.dif
/amber18/test/PIMD/part_pimd_water
--> This file is empty...
possible FAILURE: (ignored) check min.out.dif
/amber18/test/sebomd/AM1-d-CB1/dimethylether
99c99
< 4 -4.5795E+1 4.0472 7.7317 H13 5
> 4 -4.5795E+1 4.0472 7.7317 H12 4
--> Don't really know what has happened here though I assume the difference is the hydrogen atom name?
Next up is the GCC installation
Have a fantastic weekend and best regards
Best regards
// Gustaf
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Received on Sat Apr 27 2019 - 06:00:02 PDT
