So, Debian Squeeze updated to the latest patch level.
The minor version of the intel compilers 11.0 that I use is 084.
Here I report all my compilation steps:
loadModule /software/ENV/set_impi_322.sh
loadModule /software/ENV/set_intel-110.sh
setVar I_MPI_F90 ifort
setVar I_MPI_CC icc
cd /software/BUILD
cp /software/SOURCES/amber/* ./
tar jxvf Amber11.tar.bz2
tar jxvf AmberTools-1.5.tar.bz2
mv amber11 /software
export AMBERHOME=/software/amber11
cp bugfix.all /software/amber11
cd /software/amber11
patch -p0 -N < bugfix.all
/software/BUILD/apply_bugfix.x /software/BUILD/bugfix.1to17.tar.bz2
cd /software
mv amber11 amber-11-intel
export AMBERHOME=/software/amber-11-intel
cd $AMBERHOME/AmberTools/src
make clean
./configure -noX11 intel
# vim config.h
make serial
# cd ../test
# make test
cd /software/amber-11-intel
./AT15_Amber11.py
cd src
make clean
make serial
# cd ../test
# make test
cd $AMBERHOME/AmberTools/src
make clean
export MPI_HOME="/software/intel/impi/3.2.2/006"
./configure -noX11 -mpi intel
make parallel
# cd ../test
# export DO_PARALLEL='mpirun -np 4'
# make test.parallel
cd /software/amber-11-intel
./AT15_Amber11.py
cd src
make clean
make parallel
# cd ../test
# export DO_PARALLEL='mpirun -np 4'
# make test.parallel
On 09/23/11 03:10, Jason Swails wrote:
> On Thu, Sep 22, 2011 at 8:59 PM, Matteo Guglielmi
> <matteo.guglielmi.epfl.ch>wrote:
>
>> Dear All,
>>
>> I could successfully compile ambertools (serial), amber (serial)
>> and amber (parallel) using the intel compilers (11.0) and intel
>> mpi (3.2.2) on a cluster Debian Squeeze based.
>>
>
> What is the minor version number on your intel compilers? I use 11.1.069
> and it works just fine... I've never seen these error messages before.
>
>
>>
>> The compilation of ambertools (parallel) runs smoothly until it
>> reaches nab.c:
>>
>> ### ERROR MESSAGE ###
>> make[1]: Leaving directory
>> `/share/lcbc/software/amber-11-intel/AmberTools/src/pbsa'
>> (cd nab&& make parallel )
>> make[1]: Entering directory
>> `/share/lcbc/software/amber-11-intel/AmberTools/src/nab'
>> mpicc -DBINDIR='"/software/amber-11-intel/bin"' \
>> -DINCDIR='"/software/amber-11-intel/include"' \
>> -DLIBDIR='"/software/amber-11-intel/lib"' \
>> -DCC='"mpicc"' -DCPP='"/software/amber-11-intel/bin/ucpp
>> -l"'
>> -DFLIBS='"-L/software/amber-11-intel/lib -lsff_mpi -lpbsa
>> /software/amber-11-intel/lib/arpack.a
>> /software/amber-11-intel/lib/lapack.a
>> /software/amber-11-intel/lib/blas.a
>> /software/amber-11-intel/lib/libnetcdf.a
>> -L/software/intel/Compiler/11.0/084/lib/intel64/ -lifport -lifcore
>> -lsvml "' \
>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
>> \
>> -shared-intel -o /software/amber-11-intel/bin/mpinab
>> nab.c
>> nab.c(159): error: missing closing quote
>> CPP, cppstring, INCDIR,
>> ^
>>
>> nab.c(261): error: missing closing quote
>> sprintf( word, " %s ", FLIBS );
>> ^
>>
>> compilation aborted for nab.c (code 2)
>> ### END ERROR MESSAGE ###
>>
>> Any advise about this error message?
>>
>> PS: using the intel compilers 11.1 insead of 11.0 I cannot even
>> compile the serial version of ambertools... I get very similar
>> error messages which I'm not reporting here.
>>
>
>> Thanks,
>>
>> --matt
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Fri Sep 23 2011 - 02:30:02 PDT
