Greetings,
My earlier compilation of amber12 was fine in centos5.7. But I could not run pmemd.cuda.MPI because some errors in the gcc versions.
Well after some help form this forum, I tried to install amber12 again in new os (centos6.2).
I followed guide as in
http://jswails.wikidot.com/installing-amber12-and-ambertools-12 and used previous experience to install amber12. All went well until
The sequence of commands below assumes that you have already set AMBERHOME properly.
cd $AMBERHOME
./configure -mpi gnu
make install
If you wish to test this build right now, you can set the environment variable DO_PARALLEL to specify multiple threads (e.g., export DO_PARALLEL='mpirun -np 2' or export DO_PARALLEL='mpirun -np 8') and run the command
make test
When I tried to make test, I get errors as below.
My hostname is "gpucc"
***************************************************************
[root.gpucc amber12]# make test
(cd AmberTools/test && make test.parallel)
make[1]: Entering directory `/usr/local/apps/amber12/AmberTools/test'
./test_at_parallel.sh
make[2]: Entering directory `/usr/local/apps/amber12/AmberTools/test'
./test_at_clean.sh
cd mmpbsa_py && make -k clean
make[3]: Entering directory `/usr/local/apps/amber12/AmberTools/test/mmpbsa_py'
cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif
cd 01_Generalized_Born && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 02_Poisson_Boltzmann && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 03_Alanine_Scanning && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 04_Per_Residue_Decomp && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 05_Pairwise_Decomp && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 06_NAB_Nmode && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 07_Comprehensive && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv
cd 08_Stability && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv
cd 09_APBS_Poisson_Boltzmann && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 10_QM_MMGBSA && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
cd 11_3D-RISM && /usr/local/apps/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv
make[3]: Leaving directory `/usr/local/apps/amber12/AmberTools/test/mmpbsa_py'
cd cpptraj && make -k clean
make[3]: Entering directory `/usr/local/apps/amber12/AmberTools/test/cpptraj'
Cleaning all test directories:
(find . -name 'test.out' -o -name 'valgrind.out' -o -name 'Thread.*' \
-o -name 'Test_Results.dat' -o -name 'Test_Error.dat' | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
make test.complete OPT=clean
make[4]: Entering directory `/usr/local/apps/amber12/AmberTools/test/cpptraj'
make[4]: Leaving directory `/usr/local/apps/amber12/AmberTools/test/cpptraj'
make[3]: Leaving directory `/usr/local/apps/amber12/AmberTools/test/cpptraj'
cd leap/glycam && ./Run_tests.bash clean
cd nab && make -k test
make[3]: Entering directory `/usr/local/apps/amber12/AmberTools/test/nab'
Running test to do simple minimization
(this tests the molecular mechanics interface)
ssh: Could not resolve hostname gpucc: Name or service not known
*******************************************************************************
I really dont get what is wrong with "ssh".
Is there anyone can guide how to fix this issue?
Appreciate any help in advance.
Thank you
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Sun Apr 29 2012 - 01:30:03 PDT
