hi, you forget to "source amber.sh"
Hai
On Sat, Apr 27, 2019 at 8:58 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> 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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> AMBER.ambermd.org
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>
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Received on Sat Apr 27 2019 - 10:00:02 PDT
