Hi,
I installed a serial version of GMX, and am trying to install an mpi
version. I did a make distclean, and followed standard procedures, and
am getting the following errors during make mdrun:
Any suggestions ? Thank you !
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(cd ./src/gmxlib && make ; exit 0)
make[1]: Entering directory `/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib'
Making all in nonbonded
make[2]: Entering directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded'
Making all in nb_kernel_x86_64_sse
make[3]: Entering directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel_x86_64_sse'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel_x86_64_sse'
Making all in nb_kernel
make[3]: Entering directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
make all-am
make[4]: Entering directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
make[4]: Nothing to be done for `all-am'.
make[4]: Leaving directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
make[3]: Leaving directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
make[3]: Entering directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded'
/bin/sh ../../../libtool --tag=CC --mode=compile mpicc
-DHAVE_CONFIG_H -I. -I../../../src -I../../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT
nonbonded.lo -MD -MP -MF .deps/nonbonded.Tpo -c -o nonbonded.lo
nonbonded.c
mpicc -DHAVE_CONFIG_H -I. -I../../../src -I../../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT
nonbonded.lo -MD -MP -MF .deps/nonbonded.Tpo -c nonbonded.c -o
nonbonded.o
nonbonded.c: In function 'do_nonbonded':
nonbonded.c:272: error: 'esolSPC' undeclared (first use in this function)
nonbonded.c:272: error: (Each undeclared identifier is reported only once
nonbonded.c:272: error: for each function it appears in.)
nonbonded.c:276: error: 'esolTIP4P' undeclared (first use in this function)
nonbonded.c:472: error: 'enlistWATER' undeclared (first use in this function)
nonbonded.c:476: error: 'enlistWATERWATER' undeclared (first use in
this function)
nonbonded.c: In function 'do_nonbonded14':
nonbonded.c:542: error: 'eelRF_NEC' undeclared (first use in this function)
nonbonded.c:569: error: 'epbcFULL' undeclared (first use in this function)
make[3]: *** [nonbonded.lo] Error 1
make[3]: Leaving directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib/nonbonded'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/people/mail/hkhandel/gromacs-3.3.2/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/people/mail/hkhandel/gromacs-3.3.2/src/mdlib'
Makefile:249: .deps/calcmu.Plo: No such file or directory
Makefile:250: .deps/calcvir.Plo: No such file or directory
Makefile:251: .deps/clincs.Plo: No such file or directory
Makefile:252: .deps/constr.Plo: No such file or directory
Makefile:253: .deps/coupling.Plo: No such file or directory
Makefile:254: .deps/csettle.Plo: No such file or directory
Makefile:255: .deps/dummies.Plo: No such file or directory
Makefile:256: .deps/ebin.Plo: No such file or directory
Makefile:257: .deps/edsam.Plo: No such file or directory
Makefile:258: .deps/ewald.Plo: No such file or directory
Makefile:259: .deps/fftgrid.Plo: No such file or directory
Makefile:260: .deps/force.Plo: No such file or directory
Makefile:261: .deps/ghat.Plo: No such file or directory
Makefile:262: .deps/hole.Plo: No such file or directory
Makefile:263: .deps/init.Plo: No such file or directory
Makefile:264: .deps/mdatom.Plo: No such file or directory
Makefile:265: .deps/mdebin.Plo: No such file or directory
Makefile:266: .deps/minimize.Plo: No such file or directory
Makefile:267: .deps/ns.Plo: No such file or directory
Makefile:268: .deps/nsb.Plo: No such file or directory
Makefile:269: .deps/nsgrid.Plo: No such file or directory
Makefile:270: .deps/pme.Plo: No such file or directory
Makefile:271: .deps/poisson.Plo: No such file or directory
Makefile:272: .deps/pppm.Plo: No such file or directory
Makefile:273: .deps/psgather.Plo: No such file or directory
Makefile:274: .deps/pssolve.Plo: No such file or directory
Makefile:275: .deps/psspread.Plo: No such file or directory
Makefile:276: .deps/pull.Plo: No such file or directory
Makefile:277: .deps/pullinit.Plo: No such file or directory
Makefile:278: .deps/pullio.Plo: No such file or directory
Makefile:279: .deps/pullutil.Plo: No such file or directory
Makefile:280: .deps/shakef.Plo: No such file or directory
Makefile:281: .deps/sim_util.Plo: No such file or directory
Makefile:282: .deps/splittop.Plo: No such file or directory
Makefile:283: .deps/tables.Plo: No such file or directory
Makefile:284: .deps/tgroup.Plo: No such file or directory
Makefile:285: .deps/update.Plo: No such file or directory
Makefile:286: .deps/vcm.Plo: No such file or directory
Makefile:287: .deps/wnblist.Plo: No such file or directory
make[1]: *** No rule to make target `.deps/wnblist.Plo'. Stop.
make[1]: Leaving directory `/people/mail/hkhandel/gromacs-3.3.2/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory `/people/mail/hkhandel/gromacs-3.3.2/src/kernel'
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT glaasje.o
-MD -MP -MF .deps/glaasje.Tpo -c -o glaasje.o glaasje.c
mv -f .deps/glaasje.Tpo .deps/glaasje.Po
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gctio.o
-MD -MP -MF .deps/gctio.Tpo -c -o gctio.o gctio.c
gctio.c: In function 'read_gct':
gctio.c:459: warning: passing argument 4 of 'get_eenum' from
incompatible pointer type
gctio.c:460: warning: passing argument 4 of 'get_eenum' from
incompatible pointer type
mv -f .deps/gctio.Tpo .deps/gctio.Po
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT init_sh.o
-MD -MP -MF .deps/init_sh.Tpo -c -o init_sh.o init_sh.c
mv -f .deps/init_sh.Tpo .deps/init_sh.Po
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT ionize.o
-MD -MP -MF .deps/ionize.Tpo -c -o ionize.o ionize.c
mv -f .deps/ionize.Tpo .deps/ionize.Po
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/people/mail/hkhandel/gromacs-3.3.2/share/top\"
-I/people/mail/hkhandel/fftw-3.0.1/include -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT do_gct.o
-MD -MP -MF .deps/do_gct.Tpo -c -o do_gct.o do_gct.c
In file included from do_gct.c:49:
../../include/mdrun.h:56:21: error: dummies.h: No such file or directory
In file included from ../../include/mdrun.h:59,
from do_gct.c:49:
../../include/hole.h:11:19: error: binio.h: No such file or directory
../../include/hole.h:19:19: error: fatal.h: No such file or directory
In file included from do_gct.c:49:
../../include/mdrun.h:76: error: expected declaration specifiers or
'...' before 't_comm_dummies'
../../include/mdrun.h:77: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:88: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:92: error: expected declaration specifiers or
'...' before 't_comm_dummies'
../../include/mdrun.h:98: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:102: error: expected declaration specifiers or
'...' before 't_comm_dummies'
../../include/mdrun.h:109: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:121: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:172: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:191: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:206: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:216: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:233: error: expected declaration specifiers or
'...' before 't_parm'
../../include/mdrun.h:237: error: expected declaration specifiers or
'...' before 't_comm_dummies'
../../include/mdrun.h:267: error: expected declaration specifiers or
'...' before 't_parm'
In file included from do_gct.c:53:
../../include/update.h:60: error: expected declaration specifiers or
'...' before 't_parm'
make[1]: *** [do_gct.o] Error 1
make[1]: Leaving directory `/people/mail/hkhandel/gromacs-3.3.2/src/kernel'
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