Hi,
I am trying to install AMBER9 on a dual core AMD Opteron(tm) processor 275 with
4GB RAM. For serial version, only leap failed, (only tleap option also) I have
pasted the error message for leap installation failure at the very bottom of
this message.
But since leap was not that vitally needed on the cluster, i commented out the
tleap line and rest of the serial version got installed successfully and also
the test cases ran without error. For parallel version, i used
./configure -static -opteron -intelmpi ifort_x86_64
(MPI_HOME is /opt/intel/cmkl/8.1/ and MKL_HOME is /opt/intel/mpi/2.0.1/.) The
installation ran into the error that i have pasted below. To me, it looks like
the trailing underscore problem but i am not sure. Can somebody tell me what
needs to be done to get rid of this error? (And also the leap serial
installation error?)
Thanks and Regards,
Arvind
ps: I have already applied bugfix.all.
Parallel installation error for amber9:
***********************************************************************************
qm_div.o force.o \
../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
../lib/nxtsec.o ../lib/sys.a -L/opt/intel/mpi/2.0.1//lib64 -lmpi
-lmpiif -lmpigi -lrt /opt/intel/cmkl/8.1//lib/em64t/libmkl_lapack.a
/opt/intel/cmkl/8.1//lib/em64t/libmkl_em64t.a
-L/opt/intel/cmkl/8.1//lib/em64t -lguide -lpthread
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(abortf.o)(.text+0x9): In function
`mpi_abort_':
: undefined reference to `MPI_Abort'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(allgatherf.o)(.text+0x1b): In function
`mpi_allgather_':
: undefined reference to `MPI_Allgather'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(allgathervf.o)(.text+0x18): In function
`mpi_allgatherv_':: undefined reference to `MPI_Allgatherv'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(allreducef.o)(.text+0xc): In function
`mpi_allreduce_':
: undefined reference to `MPI_Allreduce'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(barrierf.o)(.text+0x8): In function
`mpi_barrier_':
: undefined reference to `MPI_Barrier'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(bcastf.o)(.text+0xf): In function
`mpi_bcast_':
: undefined reference to `MPI_Bcast'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(comm_freef.o)(.text+0x6): In function
`mpi_comm_free_':
: undefined reference to `MPI_Comm_free'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(comm_rankf.o)(.text+0x7): In function
`mpi_comm_rank_':
: undefined reference to `MPI_Comm_rank'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(comm_sizef.o)(.text+0x7): In function
`mpi_comm_size_':
: undefined reference to `MPI_Comm_size'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(comm_splitf.o)(.text+0xc): In function
`mpi_comm_split_':
: undefined reference to `MPI_Comm_split'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(finalizef.o)(.text+0x6): In function
`mpi_finalize_':
: undefined reference to `MPI_Finalize'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(gatherf.o)(.text+0x1e): In function
`mpi_gather_':
: undefined reference to `MPI_Gather'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(initf.o)(.text+0xa): In function
`mpi_init_':
: undefined reference to `MPI_Init'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(irecvf.o)(.text+0x1a): In function
`mpi_irecv_':
: undefined reference to `MPI_Irecv'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(isendf.o)(.text+0x1a): In function
`mpi_isend_':
: undefined reference to `MPI_Isend'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(recvf.o)(.text+0x2d): In function
`mpi_recv_':
: undefined reference to `MPI_Recv'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(redscatf.o)(.text+0xa): In function
`mpi_reduce_scatter_':: undefined reference to `MPI_Reduce_scatter'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(reducef.o)(.text+0x1b): In function
`mpi_reduce_':
: undefined reference to `MPI_Reduce'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(sendf.o)(.text+0xe): In function
`mpi_send_':
: undefined reference to `MPI_Send'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(sendrecvf.o)(.text+0x55): In function
`mpi_sendrecv_':
: undefined reference to `MPI_Sendrecv'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(type_commitf.o)(.text+0x6): In function
`mpi_type_commit_':
: undefined reference to `MPI_Type_commit'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(type_freef.o)(.text+0x6): In function
`mpi_type_free_':
: undefined reference to `MPI_Type_free'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(typecontigf.o)(.text+0x9): In function
`mpi_type_contiguous_':
: undefined reference to `MPI_Type_contiguous'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(waitallf.o)(.text+0x1c): In function
`mpi_waitall_':
: undefined reference to `MPI_Waitall'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(waitanyf.o)(.text+0x26): In function
`mpi_waitany_':
: undefined reference to `MPI_Waitany'
/opt/intel/mpi/2.0.1//lib64/libmpiif.a(waitf.o)(.text+0x19): In function
`mpi_wait_':
: undefined reference to `MPI_Wait'
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/soft/amber9/src/sander'
make: *** [parallel] Error 2
.....................................................................................
Amber9 serial installation error for leap
*************************************************************************************
cd leap/src/leap; make -f Makefile.tleap install
make[1]: Entering directory `/soft/amber9/src/leap/src/leap'
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o basics.o basics.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o sysdepend.o
sysdepend.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o stringExtra.o
stringExtra.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o varArray.o
varArray.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o getline.o getline.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o avl.o avl.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o pdb_format.o
pdb_format.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o pdb_read.o
pdb_read.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o pdb_sprntf.o
pdb_sprntf.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o pdb_sscanf.o
pdb_sscanf.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o pdb_write.o
pdb_write.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o vector.o vector.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o zMatrix.o zMatrix.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o sort.o sort.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o bag.o bag.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o hash.o hash.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o dictionary.o
dictionary.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o database.o
database.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o nVector.o nVector.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o ring.o ring.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o matrix.o matrix.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o fortran.o fortran.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o displayer.o
displayer.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o assoc.o assoc.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o atom.o atom.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o byteArray.o
byteArray.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o collection.o
collection.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o container.o
container.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o internal.o
internal.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o list.o list.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o loop.o loop.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o molecule.o
molecule.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o oDouble.o oDouble.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o oInteger.o
oInteger.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o oString.o oString.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o objekt.o objekt.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o parmSet.o parmSet.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o residue.o residue.c
residue.c: In function `ResidueConnect':
residue.c:336: warning: passing arg 1 of `AtomBondTo' from incompatible pointer
type
residue.c:336: warning: passing arg 2 of `AtomBondTo' from incompatible pointer
type
residue.c: In function `ResidueMutate':
residue.c:464: warning: passing arg 1 of `BuildFixInternals' from incompatible
pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o unit.o unit.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o unitio.o unitio.c
unitio.c: In function `zUnitIOSaveAmberParmFormat':
unitio.c:4047: warning: passing arg 1 of `SortByInteger' from incompatible
pointer type
unitio.c:4047: warning: passing arg 4 of `SortByInteger' from incompatible
pointer type
unitio.c: In function `zUnitIOSaveAmberParmFormat_old':
unitio.c:6055: warning: passing arg 1 of `SortByInteger' from incompatible
pointer type
unitio.c:6055: warning: passing arg 4 of `SortByInteger' from incompatible
pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o graphUtil.o
graphUtil.c
graphUtil.c: In function `GraphUtilFindAllSmallestRingsAndRingGroups':
graphUtil.c:675: warning: passing arg 1 of `SortByInteger' from incompatible
pointer type
graphUtil.c:675: warning: passing arg 4 of `SortByInteger' from incompatible
pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o select.o select.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o amber.o amber.c
amber.c: In function `uAmberReadUnitFromPrep':
amber.c:986: warning: passing arg 1 of `SortByInteger' from incompatible pointer
type
amber.c:986: warning: passing arg 4 of `SortByInteger' from incompatible pointer
type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o build.o build.c
build.c: In function `bBuildFlipChiralityFor':
build.c:1901: warning: passing arg 1 of `SortByInteger' from incompatible
pointer type
build.c:1901: warning: passing arg 4 of `SortByInteger' from incompatible
pointer type
build.c:1907: warning: passing arg 1 of `GraphUtilFindAllSmallestRings' from
incompatible pointer type
build.c: In function `BuildInternalsForSimpleRings':
build.c:2185: warning: passing arg 1 of
`GraphUtilFindAllSmallestRingsAndRingGroups' from incompatible pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o elements.o
elements.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o library.o library.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o chirality.o
chirality.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o minimizer.o
minimizer.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o model.o model.c
model.c: In function `zModelOrderAtoms':
model.c:497: warning: passing arg 1 of `Sift' from incompatible pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o parmLib.o parmLib.c
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o pdbFile.o pdbFile.c
pdbFile.c: In function `zPdbBuildCoordinatesForContainer':
pdbFile.c:1088: warning: passing arg 1 of `BuildFixInternals' from incompatible
pointer type
pdbFile.c: In function `zPdbAddAtom':
pdbFile.c:1207: warning: passing arg 1 of `BuildInternalsForContainer' from
incompatible pointer type
pdbFile.c: In function `writeTER':
pdbFile.c:1761: warning: initialization from incompatible pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o tools.o tools.c
tools.c: In function `iToolDistanceSearch':
tools.c:1643: warning: passing arg 1 of `SortByDouble' from incompatible pointer
type
tools.c:1643: warning: passing arg 4 of `SortByDouble' from incompatible pointer
type
tools.c: In function `ToolOrientPrincipleAxisAlongCoordinateAxis':
tools.c:1714: warning: passing arg 2 of `MathOpDiagonalize' from incompatible
pointer type
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 -o variables.o
variables.c
yacc parser.y
make[1]: yacc: Command not found
make[1]: *** [parser.c] Error 127
make[1]: Leaving directory `/soft/amber9/src/leap/src/leap'
make: *** [serial] Error 2
..................................................................................
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 15 2007 - 06:07:35 PDT
