>From what I can see it is the "diff" that fails, comparing the output of the test with the reference and not the actual execution of the test.
This would indicate that the problem is more likely related to your system or configuration and not the installation of amber.
Text file busy
Seems to indicate the diff/test not being able to access the necessary files. Have you set $AMBERHOME correctly? Have you installed anything using "sudo" or "su/root"?
// Gustaf
________________________________
Från: Mariana Simoes Ferreira <marianasf.biof.ufrj.br>
Skickat: den 12 mars 2020 20:57:39
Till: amber.ambermd.org
Ämne: [AMBER] AmberTools19 serial installation test errors
Hello,
I've installed AmberTools19, installing the updates recommended and
miniconda, in a Ubuntu18.04 computer and several errors occurred (displayed
below) and I don't know how to overcome them. Is there anything I should do
or worry? Is it okay for me to continue with the parallel installation?
Many thanks,
Mariana S. Ferreira
Masters in Biophysics
Institute of Biophysics Carlos Chagas Filho
Federal University of Rio de Janeiro
1) diffing irspec.dat.save with irspec.dat
./Run.gbnetcdf: 14: ./Run.gbnetcdf: ./sff: Text file busy
./Run.gbnetcdf: Program error
Makefile:49: recipe for target 'gbnetcdf_test' failed
make[3]: *** [gbnetcdf_test] Error 1
2) diffing hist.dx.save with hist.dx
./Run.rism_list: 36: ./Run.rism_list: ./sff: Text file busy
./Run.rism_list: Program error
Makefile:136: recipe for target 'rism_list' failed
make[3]: *** [rism_list] Error 1
3) ./Run.gb7: 15: ./Run.gb7: ./sff: Text file busy
./Run.gb7: Program error
Makefile:64: recipe for target 'gb7_test' failed
make[3]: *** [gb7_test] Error 1
diffing M.dat.save with M.dat
diffing perresavg.dat.save with perresavg.dat
4) diffing Strip.sorted.crd.5.save with Strip.sorted.crd.5
./Run.variable_14: 14: ./Run.variable_14: ./sff: Text file busy
./Run.variable_14: Program error
Makefile:91: recipe for target 'variable_14test' failed
make[3]: *** [variable_14test] Error 1
5) ./Run.gbsa: 15: ./Run.gbsa: ./sff: Text file busy
./Run.rattle_md: 14: ./Run.rattle_md: ./sff: Text file busy
./Run.gbsa: Program error
Makefile:55: recipe for target 'gbsa_test' failed
make[3]: *** [gbsa_test] Error 1
./Run.rattle_md: Program error
Makefile:70: recipe for target 'rattle_md_test' failed
make[3]: *** [rattle_md_test] Error 1
6) ./Run.ips: 14: ./Run.ips: ./sff: Text file busy
./Run.ips: Program error
Makefile:121: recipe for target 'ips_test' failed
make[3]: *** [ips_test] Error 1
diffing image3.crd.save with image3.crd
==============================================================
diffing oresnum.dat.save with oresnum.dat
==============================================================
diffing nhbond.dat.save with nhbond.dat
==============================================================
diffing rmatrices.dat.save with rmatrices.dat
CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test
Formal charge is 0
Name is (2R)-3,3-dimethylbutan-2-amine
./Run.gb: 15: ./Run.gb: ./sff: Text file busy
./Run.gb: Program error
Makefile:46: recipe for target 'gb_test' failed
make[3]: *** [gb_test] Error 1
7) diffing vtest.dat.9.save with vtest.dat.9
./Run.shake: 15: ./Run.shake: ./sff: Text file busy
./Run.shake: Program error
Makefile:40: recipe for target 'rattle_min_test' failed
make[3]: *** [rattle_min_test] Error 1
PASSED
==============================================================
./Run.gb8: 15: ./Run.gb8:
==============================================================
diffing hbavg.dat.save with hbavg.dat
./sff: Text file busy
./Run.gb8: Program error
Makefile:67: recipe for target 'gb8_test' failed
make[3]: *** [gb8_test] Error 1
8) ./Run.xfin: 15: ./Run.xfin: ./sff: Text file busy
==============================================================
./Run.xfin: Program error
Makefile:52: recipe for target 'xfin_test' failed
make[3]: *** [xfin_test] Error 1
diffing solvavg.dat.save with solvavg.dat
9) ./Run.gb5: 15: ./Run.gb5: ./sff: Text file busy
./Run.gb5: Program error
Makefile:61: recipe for target 'gb5_test' failed
make[3]: *** [gb5_test] Error 1
diffing nc.hp1.ca.dat.save with nc.hp1.ca.dat
10) ./Run.comprehensive: Program error
Makefile:23: recipe for target 'COMPREHENSIVE' failed
make[3]: [COMPREHENSIVE] Error 1 (ignored)
make[3]: Leaving directory '/opt/amber18/AmberTools/test/mmpbsa_py'
PASSED
11) Segmentation fault (core dumped)
./Run.pbsa: Program error
Makefile:124: recipe for target 'pbsa_test' failed
make[3]: *** [pbsa_test] Error 1
diffing crd1.dat.save with crd1.dat
diffing hausdorff.matrix.gnu.save with hausdorff.fullmatrix.gnu
12) diffing sn2_dir.dat.save with sn2_dir.dat
Segmentation fault (core dumped)
./Run.gb2: Program error
Makefile:58: recipe for target 'gb2_test' failed
make[3]: *** [gb2_test] Error 1
13) Segmentation fault (core dumped)
./Run.sff: Program error
Makefile:37: recipe for target 'sff_test' failed
make[3]: *** [sff_test] Error 1
14) getpdb: can't open file gbrna.pdb.lpdb
./Run.prm: Program error
Makefile:97: recipe for target 'prm_test' failed
make[3]: *** [prm_test] Error 1
15) CPPTRAJ: CRD(1-5) => XTC
possible FAILURE: file
/opt/amber18/AmberTools/src/FEW/examples/test/MD_resp/rec/equi/
md_nvt_red_06.in does not exist.
==============================================================
collected 9 items
../../src/pytraj/tests/test_energy/test_sander_energies.py::TestSander::test_GB
PASSED
==============================================================
possible FAILURE: file
/opt/amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/prod/
md_prod_001.in does not exist.
==============================================================
diffing ff94/all_aminonc94.top with all_aminonc94.top
********************************************************************************
TEST: /opt/amber18/AmberTools/src/cpptraj/test/Test_Cluster_RandomSieve
PASSED
possible FAILURE: file
/opt/amber18/AmberTools/src/FEW/examples/test/MD_resp/rec/prod/
md_prod_001.in does not exist.
==============================================================
/opt/amber18/AmberTools/src/FEW/examples/test/MD_resp/L51a/com/prod: No
such file or directory.
Makefile:282: recipe for target 'test.FEW' failed
make[2]: *** [test.FEW] Error 1
16) diffing d_glu.bondi.rst7.save with d_glu.bondi.rst7
make[3]: Target 'test' not remade because of errors.
17) make[3]: Target 'testrism' not remade because of errors.
make[3]: Leaving directory '/opt/amber18/AmberTools/test/nab'
Makefile:104: recipe for target 'test.nab' failed
make[2]: *** [test.nab] Error 2
PASSED
18) make[2]: Target 'test.serial' not remade because of errors.
make[2]: Leaving directory '/opt/amber18/AmberTools/test'
make[2]: Entering directory '/opt/amber18/test'
make[2]: Leaving directory '/opt/amber18/AmberTools/test'
2364 file comparisons passed
24 file comparisons failed (0 ignored)
17 tests experienced errors
Test log file saved as
/opt/amber18/logs/test_at_serial/2020-03-12_13-37-19.log
Test diffs file saved as
/opt/amber18/logs/test_at_serial/2020-03-12_13-37-19.diff
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Received on Fri Mar 13 2020 - 02:00:02 PDT
