Jennifer Williams wrote:
Hello
I know this is possibly an issue for the IT support at my Uni but I was
wondering if someone could shed some light on what may have gone wrong
so at least I can point them in the right direction.
As I am getting very small diffusion coefficients when using g_msd, I
want to increase the number of decimal points the diffusion coefficient
is displayed to.
In the file gmx_msd.c within src/tools I changed
fprintf(out,"# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n",
to
fprintf(out,"# D[%10s] = %.8f (+/- %.8f) (1e-5 cm^2/s)\n",
then, as I have always done, I just typed in make g_msd to recompile
this tool.
I get the following error message:
src/tools> make g_msd
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/home/jwillia4/GRO/share/top\"
-I/home/jwillia4/GRO/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT g_msd.o -MD
-MP -MF .deps/g_msd.Tpo -c -o g_msd.o g_msd.c
mv -f .deps/g_msd.Tpo .deps/g_msd.Po
/bin/sh ../../libtool --tag=CC --mode=link mpicc -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -L/home/jwillia4/GRO/lib -lgslcblas -o g_msd
g_msd.o libgmxana_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la
-lgsl -lnsl -lfftw3f -lm
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -o g_msd g_msd.o -L/home/jwillia4/GRO/lib
./.libs/libgmxana_mpi.a
/home/jwillia4/GRO/gromacs-4.0.7/src/mdlib/.libs/libmd_mpi.a
../mdlib/.libs/libmd_mpi.a
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a
../gmxlib/.libs/libgmx_mpi.a /home/jwillia4/GRO/lib/libgslcblas.so
/home/jwillia4/GRO/lib/libgsl.so -lnsl
/home/jwillia4/GRO/lib/libfftw3f.a -lm -Wl,--rpath
-Wl,/home/jwillia4/GRO/lib -Wl,--rpath -Wl,/home/jwillia4/GRO/lib
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o):
In function `init_par':
main.c:(.text+0xc0): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xc8): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o):
In function `init_multisystem':
main.c:(.text+0xb99): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xbd9): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xbee): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):network.c:(.text+0x15):
more undefined references to `ompi_mpi_comm_world' follow
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_sumi_sim':
network.c:(.text+0x96): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x9b): undefined reference to `ompi_mpi_int'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_sumf_sim':
network.c:(.text+0x4e6): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x4eb): undefined reference to `ompi_mpi_float'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_sumd_sim':
network.c:(.text+0x9a6): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x9ab): undefined reference to `ompi_mpi_double'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_sumi':
network.c:(.text+0xe8f): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0xe94): undefined reference to `ompi_mpi_int'
network.c:(.text+0xec0): undefined reference to `ompi_mpi_int'
network.c:(.text+0xed7): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0xedc): undefined reference to `ompi_mpi_int'
network.c:(.text+0x12fe): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1303): undefined reference to `ompi_mpi_int'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_sumf':
network.c:(.text+0x134e): undefined reference to `ompi_mpi_float'
network.c:(.text+0x1354): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1380): undefined reference to `ompi_mpi_float'
network.c:(.text+0x1397): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x139c): undefined reference to `ompi_mpi_float'
network.c:(.text+0x183e): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1843): undefined reference to `ompi_mpi_float'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_sumd':
network.c:(.text+0x1890): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1895): undefined reference to `ompi_mpi_double'
network.c:(.text+0x18c2): undefined reference to `ompi_mpi_double'
network.c:(.text+0x18d7): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x18dc): undefined reference to `ompi_mpi_double'
network.c:(.text+0x1d86): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1d8b): undefined reference to `ompi_mpi_double'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_bcast_sim':
network.c:(.text+0x1dbc): undefined reference to `ompi_mpi_byte'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_bcast':
network.c:(.text+0x1ddc): undefined reference to `ompi_mpi_byte'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_abort':
network.c:(.text+0x1e3c): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_node_num':
network.c:(.text+0x1e85): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_node_rank':
network.c:(.text+0x1ea5): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):
In function `gmx_setup':
network.c:(.text+0x2309): undefined reference to `ompi_mpi_comm_world'
network.c:(.text+0x231b): undefined reference to `ompi_mpi_comm_world'
collect2: ld returned 1 exit status
make: *** [g_msd] Error 1
The compile seems to need some mpi files but shouldn't the tools compile
in serial rather than parallel? I have recompiled in tools before and
everything has worked previously. Any advice appreciated.
Absolutely. The only Gromacs tool that is MPI-aware is mdrun. It looks like
the Makefile that you generated to do this compilation was created with
--enable-mpi. Try again using a normal C compiler like gcc.
-Justin
Thanks
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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