I'm trying to install a local copy of GROMACS on Ohio Super Computer.<br>I was able to build single and double precision versions (did 'make<br>distclean' after each), however, got errors while installing parallel<br>
version.<br>
<br>I will appreciate you taking time to help with this installation. Thanks.<br><br>This is what I did:<br><br>export CPPFLAGS=$FFTW_CFLAGS<br>export LDFLAGS=$FFTW_LIBS<br><br>****contents of FFTW_CFLAGS=-I/usr/local/<div id=":1e4" class="ii gt">
fftw3-3.1.2/include<br>
fftw3.f fftw3.h<br><br>***contents of FFTW_LIBS=-L/usr/local/fftw3-3.1.2/lib -lfftw3 -lfftw3f -lm<br>libfftw3.a libfftw3f.so <a href="http://libfftw3.la/" target="_blank">libfftw3.la</a> libfftw3.so.3.1.2<br>
libfftw3f.a libfftw3f.so.3 libfftw3.so pkgconfig<br>
<a href="http://libfftw3f.la/" target="_blank">libfftw3f.la</a> libfftw3f.so.3.1.2 libfftw3.so.3<br><br>Below I've highlighted the possible error statements I could find in output from 'configure' and 'make mdrun'<br>
<br><b>***output from './configure --enable-mpi</b><br>--prefix=/nfs/18/cwr0350/my_gromacs/gromacs_1_bin<br>--program-suffix=_mpi &>config.out'<br><br>checking build system type... x86_64-unknown-linux-gnu<br>
checking host system type... x86_64-unknown-linux-gnu<br>checking for a BSD-compatible install... /usr/bin/install -c<br>checking whether build environment is sane... yes<br>checking for a thread-safe mkdir -p... /bin/mkdir -p<br>
checking for gawk... gawk<br>checking whether make sets $(MAKE)... yes<br>checking how to create a ustar tar archive... gnutar<br>checking for cc... cc<br>checking for C compiler default output file name... a.out<br>checking whether the C compiler works... yes<br>
checking whether we are cross compiling... no<br>checking for suffix of executables...<br>checking for suffix of object files... o<br>checking whether we are using the GNU C compiler... yes<br>checking whether cc accepts -g... yes<br>
checking for cc option to accept ISO C89... none needed<br>checking for style of include used by make... GNU<br>checking dependency style of cc... gcc3<br>checking dependency style of cc... gcc3<br>checking for mpxlc... no<br>
checking for mpicc... mpicc<br>checking whether the MPI cc command works... yes<br>checking for catamount... no<br>checking how to run the C preprocessor... mpicc -E<br>checking whether mpicc accepts -O3... yes<br>checking whether mpicc accepts -funroll-all-loops... no<br>
checking whether mpicc accepts -std=gnu99... no<br><b>->->-> checking whether mpicc accepts -fast -pc 32 -O3 -fomit-frame-pointer<br>-finline-functions -Wall -Wno-unused... no<br>*******************************************************************<br>
* Sorry, these optimization settings don't seem to work for *<br>* your C compiler. Use make CFLAGS=..., or edit the top Makefile. *<br>*******************************************************************</b><br>
checking for grep that handles long lines and -e... /bin/grep<br>checking for egrep... /bin/grep -E<br>checking for ANSI C header files... yes<br>checking for sys/types.h... yes<br>checking for sys/stat.h... yes<br>checking for stdlib.h... yes<br>
checking for string.h... yes<br>checking for memory.h... yes<br>checking for strings.h... yes<br>checking for inttypes.h... yes<br>checking for stdint.h... yes<br>checking for unistd.h... yes<br>checking whether byte ordering is bigendian... no<br>
checking for int... yes<br>checking size of int... 4<br>checking for long int... yes<br>checking size of long int... 8<br>checking for long long int... yes<br>checking size of long long int... 8<br>checking for off_t... yes<br>
checking size of off_t... 8<br>checking that size_t can hold pointers... yes<br>checking floating-point format... IEEE754 (little-endian byte and word order)<br>checking for a BSD-compatible install... /usr/bin/install -c<br>
checking whether ln -s works... yes<br>checking whether make sets $(MAKE)... (cached) yes<br>checking for a sed that does not truncate output... /bin/sed<br>checking for ld used by mpicc... /usr/bin/ld<br>checking if the linker (/usr/bin/ld) is GNU ld... yes<br>
checking for /usr/bin/ld option to reload object files... -r<br>checking for BSD-compatible nm... /usr/bin/nm -B<br>checking how to recognise dependent libraries... pass_all<br>checking dlfcn.h usability... yes<br>checking dlfcn.h presence... yes<br>
checking for dlfcn.h... yes<br>checking for g++... g++<br>checking whether we are using the GNU C++ compiler... yes<br>checking whether g++ accepts -g... yes<br>checking dependency style of g++... gcc3<br>checking how to run the C++ preprocessor... g++ -E<br>
checking the maximum length of command line arguments... 32768<br>checking command to parse /usr/bin/nm -B output from mpicc object... ok<br>checking for objdir... .libs<br>checking for ar... ar<br>checking for ranlib... ranlib<br>
checking for strip... strip<br>checking if mpicc supports -fno-rtti -fno-exceptions... no<br>checking for mpicc option to produce PIC... -fPIC<br>checking if mpicc PIC flag -fPIC works... yes<br>checking if mpicc static flag -static works... no<br>
checking if mpicc supports -c -o file.o... yes<br>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports<br>shared libraries... yes<br>checking dynamic linker characteristics... pgcc-Warning-Unknown<br>switch: -print-search-dirs<br>
/usr/lib64/crt1.o: In function `_start':<br>(.text+0x20): undefined reference to `main'<br>GNU/Linux ld.so<br>checking how to hardcode library paths into programs... immediate<br>checking whether stripping libraries is possible... yes<br>
checking if libtool supports shared libraries... yes<br>checking whether to build shared libraries... no<br>checking whether to build static libraries... yes<br>configure: creating libtool<br>appending configuration tag "CXX" to libtool<br>
checking for ld used by g++... /usr/bin/ld -m elf_x86_64<br>checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes<br>checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports<br>shared libraries... yes<br>
checking for g++ option to produce PIC... -fPIC<br>checking if g++ PIC flag -fPIC works... yes<br>checking if g++ static flag -static works... yes<br>checking if g++ supports -c -o file.o... yes<br>checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports<br>
shared libraries... yes<br>checking dynamic linker characteristics... GNU/Linux ld.so<br>checking how to hardcode library paths into programs... immediate<br>appending configuration tag "F77" to libtool<br>checking for special C compiler options needed for large files... no<br>
checking for _FILE_OFFSET_BITS value needed for large files... no<br>checking for _LARGEFILE_SOURCE value needed for large files... no<br>checking for sqrt in -lm... yes<br>checking for fftw3.h... yes<br>checking for main in -lfftw3f... yes<br>
checking rpc/rpc.h usability... yes<br>checking rpc/rpc.h presence... yes<br>checking for rpc/rpc.h... yes<br>checking for rpc/xdr.h... yes<br>checking for xdr_float in -lnsl... yes<br>checking for working memcmp... yes<br>
checking return type of signal handlers... void<br>checking for off_t... (cached) yes<br>checking for vprintf... yes<br>checking for _doprnt... no<br>checking if malloc debugging is wanted... no<br>checking for strcasecmp... yes<br>
checking for strdup... yes<br>checking for bool... no<br>checking for X... libraries , headers<br>checking for gethostbyname... yes<br>checking for connect... yes<br>checking for remove... yes<br>checking for shmat... yes<br>
checking for IceConnectionNumber in -lICE... yes<br>checking libxml/parser.h usability... yes<br>checking libxml/parser.h presence... yes<br>checking for libxml/parser.h... yes<br>checking for main in -lxml2... yes<br>checking limits.h usability... yes<br>
checking limits.h presence... yes<br>checking for limits.h... yes<br>checking for strings.h... (cached) yes<br>checking for unistd.h... (cached) yes<br>checking for unistd.h... (cached) yes<br>checking for an ANSI C-conforming const... yes<br>
checking for size_t... yes<br>checking whether struct tm is in sys/time.h or time.h... time.h<br>checking for uid_t in sys/types.h... yes<br>checking for inline... inline<br>checking whether your compiler can handle assembly files (*.s)... yes<br>
checking whether as fully supports X86_64 SSE instructions... yes<br>checking whether byte ordering is bigendian... (cached) no<br>configure: creating ./config.status<br>config.status: creating Makefile<br>config.status: creating src/Makefile<br>
config.status: creating src/gmxlib/Makefile<br>config.status: creating src/gmxlib/gmx_blas/Makefile<br>config.status: creating src/gmxlib/gmx_lapack/Makefile<br>config.status: creating src/gmxlib/nonbonded/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile<br>
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile<br>
config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile<br>
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile<br>config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile<br>
config.status: creating include/Makefile<br>config.status: creating include/types/Makefile<br>config.status: creating src/mdlib/Makefile<br>config.status: creating src/kernel/Makefile<br>config.status: creating src/tools/Makefile<br>
config.status: creating src/ngmx/Makefile<br>config.status: creating src/contrib/Makefile<br>config.status: creating scripts/Makefile<br>config.status: creating admin/Makefile<br>config.status: creating share/Makefile<br>
config.status: creating share/tutor/Makefile<br>config.status: creating share/tutor/gmxdemo/Makefile<br>config.status: creating share/tutor/nmr1/Makefile<br>config.status: creating share/tutor/nmr2/Makefile<br>config.status: creating share/tutor/water/Makefile<br>
config.status: creating share/tutor/mixed/Makefile<br>config.status: creating share/tutor/methanol/Makefile<br>config.status: creating share/tutor/speptide/Makefile<br>config.status: creating share/template/Makefile<br>config.status: creating share/top/Makefile<br>
config.status: creating share/html/Makefile<br>config.status: creating share/html/images/Makefile<br>config.status: creating share/html/online/Makefile<br>config.status: creating man/Makefile<br>config.status: creating man/man1/Makefile<br>
config.status: creating src/config.h<br>config.status: executing depfiles commands<br><br><b>*******output from make mdrun &> log</b><br>(cd ./src/gmxlib && make ; exit 0)<br>make[1]: Entering directory<br>
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib'<br>Making all in nonbonded<br>
make[2]: Entering directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded'<br>Making all in nb_kernel_x86_64_sse<br>make[3]: Entering directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel_x86_64_sse'<br>
/bin/sh ../../../../libtool --tag=CC --mode=link mpicc<br>-L/usr/local/fftw3-3.1.2/lib -lfftw3 -lfftw3f -lm -o<br><a href="http://libnb_kernel_x86_64_sse.la/" target="_blank">libnb_kernel_x86_64_sse.la</a> nb_kernel010_x86_64_sse.lo<br>
nb_kernel030_x86_64_sse.lo nb_kernel100_x86_64_sse.lo<br>nb_kernel101_x86_64_sse.lo nb_kernel102_x86_64_sse.lo<br>nb_kernel103_x86_64_sse.lo nb_kernel104_x86_64_sse.lo<br>nb_kernel110_x86_64_sse.lo nb_kernel111_x86_64_sse.lo<br>
nb_kernel112_x86_64_sse.lo nb_kernel113_x86_64_sse.lo<br>nb_kernel114_x86_64_sse.lo nb_kernel130_x86_64_sse.lo<br>nb_kernel131_x86_64_sse.lo nb_kernel132_x86_64_sse.lo<br>nb_kernel133_x86_64_sse.lo nb_kernel134_x86_64_sse.lo<br>
nb_kernel200_x86_64_sse.lo nb_kernel201_x86_64_sse.lo<br>nb_kernel202_x86_64_sse.lo nb_kernel203_x86_64_sse.lo<br>nb_kernel204_x86_64_sse.lo nb_kernel210_x86_64_sse.lo<br>nb_kernel211_x86_64_sse.lo nb_kernel212_x86_64_sse.lo<br>
nb_kernel213_x86_64_sse.lo nb_kernel214_x86_64_sse.lo<br>nb_kernel230_x86_64_sse.lo nb_kernel231_x86_64_sse.lo<br>nb_kernel232_x86_64_sse.lo nb_kernel233_x86_64_sse.lo<br>nb_kernel234_x86_64_sse.lo nb_kernel300_x86_64_sse.lo<br>
nb_kernel301_x86_64_sse.lo nb_kernel302_x86_64_sse.lo<br>nb_kernel303_x86_64_sse.lo nb_kernel304_x86_64_sse.lo<br>nb_kernel310_x86_64_sse.lo nb_kernel311_x86_64_sse.lo<br>nb_kernel312_x86_64_sse.lo nb_kernel313_x86_64_sse.lo<br>
nb_kernel314_x86_64_sse.lo nb_kernel330_x86_64_sse.lo<br>nb_kernel331_x86_64_sse.lo nb_kernel332_x86_64_sse.lo<br>nb_kernel333_x86_64_sse.lo nb_kernel334_x86_64_sse.lo<br>nb_kernel400_x86_64_sse.lo nb_kernel410_x86_64_sse.lo<br>
nb_kernel430_x86_64_sse.lo nb_kernel_x86_64_sse_test_asm.lo<br>nb_kernel_x86_64_sse.lo -lxml2 -lnsl -lfftw3f -lm -lSM -lICE -lX11<br>mkdir .libs<br>ar cru .libs/libnb_kernel_x86_64_sse.a nb_kernel010_x86_64_sse.o<br>
nb_kernel030_x86_64_sse.o nb_kernel100_x86_64_sse.o<br>nb_kernel101_x86_64_sse.o nb_kernel102_x86_64_sse.o<br>nb_kernel103_x86_64_sse.o nb_kernel104_x86_64_sse.o<br>nb_kernel110_x86_64_sse.o nb_kernel111_x86_64_sse.o<br>
nb_kernel112_x86_64_sse.o nb_kernel113_x86_64_sse.o<br>
nb_kernel114_x86_64_sse.o nb_kernel130_x86_64_sse.o<br>nb_kernel131_x86_64_sse.o nb_kernel132_x86_64_sse.o<br>nb_kernel133_x86_64_sse.o nb_kernel134_x86_64_sse.o<br>nb_kernel200_x86_64_sse.o nb_kernel201_x86_64_sse.o<br>
nb_kernel202_x86_64_sse.o nb_kernel203_x86_64_sse.o<br>
nb_kernel204_x86_64_sse.o nb_kernel210_x86_64_sse.o<br>nb_kernel211_x86_64_sse.o nb_kernel212_x86_64_sse.o<br>nb_kernel213_x86_64_sse.o nb_kernel214_x86_64_sse.o<br>nb_kernel230_x86_64_sse.o nb_kernel231_x86_64_sse.o<br>
nb_kernel232_x86_64_sse.o nb_kernel233_x86_64_sse.o<br>
nb_kernel234_x86_64_sse.o nb_kernel300_x86_64_sse.o<br>nb_kernel301_x86_64_sse.o nb_kernel302_x86_64_sse.o<br>nb_kernel303_x86_64_sse.o nb_kernel304_x86_64_sse.o<br>nb_kernel310_x86_64_sse.o nb_kernel311_x86_64_sse.o<br>
nb_kernel312_x86_64_sse.o nb_kernel313_x86_64_sse.o<br>
nb_kernel314_x86_64_sse.o nb_kernel330_x86_64_sse.o<br>nb_kernel331_x86_64_sse.o nb_kernel332_x86_64_sse.o<br>nb_kernel333_x86_64_sse.o nb_kernel334_x86_64_sse.o<br>nb_kernel400_x86_64_sse.o nb_kernel410_x86_64_sse.o<br>
nb_kernel430_x86_64_sse.o nb_kernel_x86_64_sse_test_asm.o<br>
nb_kernel_x86_64_sse.o<br>ranlib .libs/libnb_kernel_x86_64_sse.a<br>creating <a href="http://libnb_kernel_x86_64_sse.la/" target="_blank">libnb_kernel_x86_64_sse.la</a><br>(cd .libs && rm -f <a href="http://libnb_kernel_x86_64_sse.la/" target="_blank">libnb_kernel_x86_64_sse.la</a> && ln -s<br>
../<a href="http://libnb_kernel_x86_64_sse.la/" target="_blank">libnb_kernel_x86_64_sse.la</a> <a href="http://libnb_kernel_x86_64_sse.la/" target="_blank">libnb_kernel_x86_64_sse.la</a>)<br>make[3]: Leaving directory<br>
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel_x86_64_sse'<br>
Making all in nb_kernel<br>make[3]: Entering directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'<br>cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb.o mknb.c<br>cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_metacode.o mknb_metacode.c<br>
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_common.o mknb_common.c<br>cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_declarations.o<br>mknb_declarations.c<br>cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_outerloop.o mknb_outerloop.c<br>
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_innerloop.o mknb_innerloop.c<br>cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_interactions.o<br>mknb_interactions.c<br>cc -DHAVE_CONFIG_H -I. -I../../../../src -o mknb mknb.o<br>
mknb_metacode.o mknb_common.o mknb_declarations.o mknb_outerloop.o<br>mknb_innerloop.o mknb_interactions.o<br>rm -f kernel-stamp<br>./mknb -software_invsqrt<br>>>> Gromacs nonbonded kernel generator (-h for help)<br>
>>> Generating single precision functions in C.<br>>>> Using Gromacs software version of 1/sqrt(x).<br><br> make all-am<br>make[4]: Entering directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'<br>
/bin/sh ../../../../libtool --tag=CC --mode=compile mpicc<br>-DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2<br>-I../../../../include<br>-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"<br>
-I/usr/local/fftw3-3.1.2/include -MT nb_kernel.lo -MD -MP -MF<br>.deps/nb_kernel.Tpo -c -o nb_kernel.lo nb_kernel.c<br> mpicc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2<br>-I../../../../include<br>-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"<br>
-I/usr/local/fftw3-3.1.2/include -MT nb_kernel.lo -MD -MP -MF<br>.deps/nb_kernel.Tpo -c nb_kernel.c -o nb_kernel.o<br>pgcc-Warning-Unknown switch: -MT<br>pgcc-Warning-Unknown switch: -MP<br>pgcc-Warning-Unknown switch: -MF<br>
File with unknown suffix passed to linker: .deps/nb_kernel.Tpo<br>nb_kernel.c:<br>mv -f .deps/nb_kernel.Tpo .deps/nb_kernel.Plo<br><b>->->->mv: cannot stat `.deps/nb_kernel.Tpo': No such file or directory<br>
make[4]: *** [nb_kernel.lo] Error 1</b><br>
<b>make[4]: Leaving directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'<br>make[3]: *** [all] Error 2<br>make[3]: Leaving directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'<br>
make[2]: *** [all-recursive] Error 1<br>make[2]: Leaving directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded'<br>make[1]: *** [all-recursive] Error 1</b><br>make[1]: Leaving directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib'<br>
(cd ./src/mdlib && make ; exit 0)<br>make[1]: Entering directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/mdlib'<br>/bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H<br>-I. -I../../src -I/usr/include/libxml2 -I../../include<br>
-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"<br>-I/usr/local/fftw3-3.1.2/include -MT calcvir.lo -MD -MP -MF<br>.deps/calcvir.Tpo -c -o calcvir.lo calcvir.c<br> mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2<br>
-I../../include<br>-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"<br>-I/usr/local/fftw3-3.1.2/include -MT calcvir.lo -MD -MP -MF<br>.deps/calcvir.Tpo -c calcvir.c -o calcvir.o<br>pgcc-Warning-Unknown switch: -MT<br>
pgcc-Warning-Unknown switch: -MP<br>pgcc-Warning-Unknown switch: -MF<br>File with unknown suffix passed to linker: .deps/calcvir.Tpo<br>calcvir.c:<br><b>->->->mv -f .deps/calcvir.Tpo .deps/calcvir.Plo<br>mv: cannot stat `.deps/calcvir.Tpo': No such file or directory<br>
make[1]: *** [calcvir.lo] Error 1</b><br>make[1]: Leaving directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/mdlib'<br>(cd ./src/kernel && make mdrun ; exit 0)<br>make[1]: Entering directory<br>`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/kernel'<br>
mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2<br>-I../../include<br>-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"<br>-I/usr/local/fftw3-3.1.2/include -MT glaasje.o -MD -MP -MF<br>
.deps/glaasje.Tpo -c -o glaasje.o glaasje.c<br>pgcc-Warning-Unknown switch: -MT<br>pgcc-Warning-Unknown switch: -MP<br>pgcc-Warning-Unknown switch: -MF<br><b>->->->pgcc-Error-Output would overwrite input file: glaasje.o<br>
make[1]: *** [glaasje.o] Error 1</b><br>
make[1]: Leaving directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/kernel'
</div>