Dear Sir,
Thanks so much for your indication. I could overcome the problem ready.
Acutally I follow the steps as described in this webside:-
http://jswails.wikidot.com/installing-amber12-and-ambertools-12
I tried to compile the serial version of amber12 and I installed openmpi-1.5.4. from Ambertools/src by executing ./configure-openmpi script. All the installation went on smoothly.
Then in execute 'make install' command to install amber12 parallel version and I got stuck again. The errors are as below;
************************************************************************
make[2]: Entering directory `/usr/local/apps/amber12/AmberTools/src/ucpp-1.3'
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE mem.c
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE nhash.c
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE cpp.c
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE lexer.c
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE assert.c
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE macro.c
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DSTAND_ALONE eval.c
mpicc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
mv ucpp /usr/local/apps/amber12/bin
make[2]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/ucpp-1.3'
(if [ "no" = "yes" ]; then \
cd rism && make install_mpi ; \
fi; \
)
(cd nab && make install )
make[2]: Entering directory `/usr/local/apps/amber12/AmberTools/src/nab'
mpicc -DCC='"mpicc"' -DCPP='"ucpp -l"' -DFLIBS='"-lsff_mpi -lpbsa -larpack -llapack -lblas -L/usr/local/apps/amber12/lib -lnetcdf -lgfortran -w "' \
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI \
-o /usr/local/apps/amber12/bin/mpinab nab.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o nab2c.o nab2c.c
flex nablex.l
/usr/local/apps/amber12/bin/yacc -d nabgrm.y
/usr/local/apps/amber12/bin/yacc: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
make[2]: *** [y.tab.c] Error 127
make[2]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/nab'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/usr/local/apps/amber12/AmberTools/src'
make: *** [install] Error 2
[root.gpucc amber12]#
**********************************************************************
Is there any chance to fix this issue?
Thank you.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: javacfish <javacfish.yahoo.com.cn>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 16 April 2012, 17:15
Subject: Re: [AMBER] error installing Amber12-gpu version
You should check g++ correctly, because the err is
make[3]: g++: Command not found
javacfish
________________________________
From: Vijay Manickam Achari <vjrajamany.yahoo.com>
To: Amber mailing List <AMBER.ambermd.org>; Amber Scrops <amber.scripps.edu>
Sent: Monday, April 16, 2012 4:25 PM
Subject: [AMBER] error installing Amber12-gpu version
We are trying to install amber12-gpu version in gpu TESLA-2075 model in Centos 5.7.
We have uninstalled gcc4.12 version and installed gcc44-g++ version and installed gfortran44 and made soft link to gfortran.
The compilation was going fine and after some time it stopped saying error.
I am posting the error here so that I could get some help.
**************************************************************************
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/usr/local/apps/amber12/include -o actions.o actions.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/usr/local/apps/amber12/include -o analyze.o analyze.c
gfortran -DBINTRAJ -c -ffree-form -O3 -mtune=native -I/usr/local/apps/amber12/include -I/usr/local/apps/amber12/include -o thermo.o thermo.F90
gfortran -DBINTRAJ -c -ffree-form -O3 -mtune=native -I/usr/local/apps/amber12/include -I/usr/local/apps/amber12/include -o pubfft.o pubfft.F90
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/usr/local/apps/amber12/include -o cluster.o cluster.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/usr/local/apps/amber12/include -o clusterLib.o clusterLib.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ \
-o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o -L/usr/local/apps/amber12/lib -lpdb -larpack -llapack -lblas -lgfortran -w -L/usr/local/apps/amber12/lib -lnetcdf -lm
cd ../lapack && make install
make[3]: Entering directory `/usr/local/apps/amber12/AmberTools/src/lapack'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/lapack'
cd ../blas && make install
make[3]: Entering directory `/usr/local/apps/amber12/AmberTools/src/blas'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/blas'
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ \
-o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o -L/usr/local/apps/amber12/lib -lpdb -larpack -llapack -lblas -lgfortran -w -L/usr/local/apps/amber12/lib -lnetcdf -lm
/bin/mv rdparm ptraj /usr/local/apps/amber12/bin
make[2]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/ptraj'
(cd cpptraj && make install)
make[2]: Entering directory `/usr/local/apps/amber12/AmberTools/src/cpptraj'
cd src && make -f Makefile_at install
make[3]: Entering directory `/usr/local/apps/amber12/AmberTools/src/cpptraj/src'
g++ -c -I/usr/local/apps/amber12/include -O3 -mtune=native -DBINTRAJ -DHASGZ -DHASBZ2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/usr/local/apps/amber12/include -o main.o main.cpp
make[3]: g++: Command not found
make[3]: *** [main.o] Error 127
make[3]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/cpptraj/src'
make[2]: *** [install] Error 2
make[2]: Leaving directory `/usr/local/apps/amber12/AmberTools/src/cpptraj'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/usr/local/apps/amber12/AmberTools/src'
make: *** [install] Error 2
[root.gpucc amber12]#
***************************************************************************
Thank you in advance.
Vijay Manickam Achari
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Mon Apr 16 2012 - 06:00:03 PDT
