Hi,
I've been trying to install AmberTools18 following the steps in the manual
(section 2, steps 1-7, selecting as compiler gnu) in my Ubuntu 18.04.2 LTS,
all up to date packages. However, I've been getting failures and errors
when I run make test (at serial, later I want to install the parallel
option as well). Attached there are the test log and diff files.
2204 file comparisons passed
2 file comparisons failed
6 tests experienced errors
>From the Test log file, failures are the following:
1) cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g
diffing h2o.blyp_sto-3g.out.save with h2o.blyp_sto-3g.out
possible FAILURE: check h2o.blyp_sto-3g.out.dif
==============================================================
2) cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g_md
diffing h2o.blyp_sto-3g_md.out.save with h2o.blyp_sto-3g_md.out
possible FAILURE: check h2o.blyp_sto-3g_md.out.dif
>From the Test log file, errors are the following:
1) TEST:
/home/marianasf/amber18/AmberTools/src/cpptraj/test/Test_FixAtomOrder
CPPTRAJ: Out of order molecules test (will print error messages)
Error: Atom 45 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing, or if
the
Error: atom numbering in molecules is not sequential. Try one of the
Error: following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error: associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error: topology.
Error: Could not determine molecule information for outoforder.parm7.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for outoforder.parm7.
diffing reorder.outoforder.parm7.save with reorder.outoforder.parm7
2)
if [ -n "testrism" ]; then cd ./rism1d/spc-kh && ./Run.spc; fi
ERROR> could not open ../../../../dat/rism1d/model/SPC.mdl: 2
STOP 1
./Run.spc: Program error
Makefile:224: recipe for target 'test.rism1d' failed
make[2]: [test.rism1d] Error 1 (ignored)
if [ -n "testrism" ]; then cd ./rism1d/spc-psen && ./Run.spc-nacl-3; fi
ERROR> could not open ../../../../dat/rism1d/model/SPC.mdl: 2
STOP 1
./Run.spc-nacl-3: Program error
Makefile:224: recipe for target 'test.rism1d' failed
make[2]: [test.rism1d] Error 1 (ignored)
if [ -n "testrism" ]; then cd ./rism1d/spc-hnc && ./Run.spc-lj; fi
ERROR> could not open ../../../../dat/rism1d/model/SPC.mdl: 2
STOP 1
./Run.spc-lj: Program error
Makefile:224: recipe for target 'test.rism1d' failed
make[2]: [test.rism1d] Error 1 (ignored)
if [ -n "" ]; then cd ./rism1d/spc-polyt && ./Run.spc; fi
if [ -n "testrism" ]; then cd ./rism1d/spc-mv0 && ./Run.spc; fi
ERROR> could not open ../../../../dat/rism1d/model/SPC.mdl: 2
STOP 1
./Run.spc: Program error
Makefile:224: recipe for target 'test.rism1d' failed
make[2]: [test.rism1d] Error 1 (ignored)
if [ -n "testrism" ]; then cd ./rism1d/lj-py && ./Run.lj; fi
diffing lj.xvv.delhv0.save with lj.xvv.delhv0
3) if [ -n "testrism" ]; then cd ./rism1d/tip3p-kh && ./Run.tip3p; fi
ERROR> could not open ../../../../dat/rism1d/model/TP3.mdl: 2
STOP 1
./Run.tip3p: Program error
Makefile:224: recipe for target 'test.rism1d' failed
make[2]: [test.rism1d] Error 1 (ignored)
cd rism3d.periodic/PH4+ && ./Run.PH4+.kh.pme
diffing PH4+.kh.pme.r3d.save with PH4+.kh.pme.r3d
4) cd qmmm_EXTERN/QMMM_MD_NWChem && ./Run.aladip.hf_sto-3g
Error no. 1 in getmem memory overflow : call no.,
amount requested : 84 75250
./Run.aladip.hf_sto-3g: Program error
Makefile:678: recipe for target 'test.sander.EXTERN' failed
make[2]: [test.sander.EXTERN] Error 1 (ignored)
5) cd sanderapi && make test
make[3]: Entering directory '/home/marianasf/amber18/test/sanderapi'
(if [ -f "/home/marianasf/amber18//lib/libsander.so" ]; then \
make test_all; \
else \
make test_none; \
fi;)
make[4]: Entering directory '/home/marianasf/amber18/test/sanderapi'
Creating the bad prmtop test.parm7
Testing the Fortran API
gfortran -fPIC -I/home/marianasf/amber18//include
-I/home/marianasf/amber18//include -I/home/marianasf/amber18//include
-L/home/marianasf/amber18//lib test.F90 -o testf -lsander
Running testf
Checking proper treatment of a bad prmtop
ERROR: Flag "ATOM_NAME" not found in PARM file
6) Testing the C API
gcc -fPIC -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
-DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN
-I/home/marianasf/amber18//include -L/home/marianasf/amber18//lib test.c
-o testc -lsander
Running testc
Testing proper treatment of a bad prmtop
ERROR: Flag "ATOM_NAME" not found in PARM file
Thanks,
Mariana S Ferreira
Masters in Biophysics - UFRJ
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Received on Wed Mar 20 2019 - 10:30:02 PDT
