I am trying to install gromacs with MPI enabled on a cluster but it seems like
fftw is giving me trouble.
First, I compile everything without MPI just fine. FFTW is already on the
cluster. I export pertinent variables...
export CPPFLAGS=-I/opt/fftw/3.2.1/include
export LDFLAGS=-L/opt/fftw/3.2.1/lib
export CC=/opt/intel/Compiler/11.1/069/bin/intel64/icc
export F77=/opt/intel/Compiler/11.1/069/bin/intel64/ifort
I have been using gromacs without MPI for over a month without any issues. Now,
I need to recompile mdrun with MPI. So I use...
export MPICC=/opt/intel/mpi/3.1/bin64/mpicc
in addition to all the previous exports. Then, I issue the command...
>./configure --prefix=/home/username/gromacs --enable-mpi --program-suffix=_mpi
>--disable-nice --enable-double
which runs fine. Then I issue...
>make mdrun
and I end up with a bunch of undefined references. I am copying some of the
output here. Also, I do not know if FFTW is compiled with single/double because
of unresponsive admins, but I have tried compiling gromacs with both options
and still got errors. Also, from a previous post, I read the idea to install
FFTW with shared libraries enabled, which I tried but just ended up with other
errors. Thanks in advance for any help. I have been at this for weeks.
By the way, this might not be critical, but here is some system info
# 2 Nodes Share:
* 1x 1702 Altus Server (1U, contains 2 Independent Motherboards)
# 1x AMD Dual Opteron 2380(Shanghai) 2.5GHz Quad Core (8 Cores)
# 250GB SATA2 Hard Drive
*****output from "make mdrun" ******
/opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x649):
more undefined references to `_inte
l_fast_memcpy' follow
/opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o): In function `apply_toms513':
vrank3-transpose.c:(.text+0xe3e): undefined reference to `_intel_fast_memset'
vrank3-transpose.c:(.text+0xef4): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0xf0e): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x106d): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x108a): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x110d): undefined reference to `_intel_fast_memcpy'
/opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1122):
more undefined references to `_int
el_fast_memcpy' follow
/opt/fftw/3.2.1/lib/libfftw3.a(dht-rader.o): In function `apply':
dht-rader.c:(.text+0x4a8): undefined reference to `_intel_fast_memset'
/opt/fftw/3.2.1/lib/libfftw3.a(dht-rader.o): In function `awake':
dht-rader.c:(.text+0xaab): undefined reference to `_intel_fast_memset'
/opt/fftw/3.2.1/lib/libfftw3.a(cpy1d.o): In function `fftw_cpy1d':
cpy1d.c:(.text+0x268): undefined reference to `_intel_fast_memcpy'
/opt/fftw/3.2.1/lib/libfftw3.a(cpy2d.o): In function `dotile_buf':
cpy2d.c:(.text+0x6a7): undefined reference to `_intel_fast_memcpy'
cpy2d.c:(.text+0x129f): undefined reference to `_intel_fast_memcpy'
cpy2d.c:(.text+0x1870): undefined reference to `_intel_fast_memcpy'
cpy2d.c:(.text+0x1902): undefined reference to `_intel_fast_memcpy'
/opt/fftw/3.2.1/lib/libfftw3.a(cpy2d.o):cpy2d.c:(.text+0x22dd): more undefined
references to `_intel_fast_memcpy' follow
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Unpack_external'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Win_get_errhandler'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_start'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_test'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_spawn'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Request_get_status'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`MPIR_Err_return_comm'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_dup'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Win_get_group'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Comm_spawn_multiple'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Free_mem'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`MPIR_Grequest_set_lang_f77'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Win_create_keyval'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`b_use_gettimeofday'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Type_get_attr'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Close_port'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Comm_create_errhandler'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Query_thread'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Type_match_size'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Open_port'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Win_set_attr'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_fence'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPID_Wtick'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Comm_set_errhandler'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`MPIR_Err_create_code'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Type_set_name'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Grequest_complete'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Add_error_class'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Type_delete_attr'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Accumulate'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Type_create_hindexed'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Alltoallw'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Win_create_errhandler'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`MPI_F_STATUSES_IGNORE'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_post'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Comm_get_attr'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Add_error_code'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Comm_call_errhandler'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Type_get_extent'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Publish_name'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Comm_disconnect'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Get'
/opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to
`PMPI_Unpublish_name'
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