[gmx-users] Gromacs Installation error
Hi gromacs users,
Iam trying to install gromacs on IBM cluster. I have successfully installed
installed fftw-3.3 version with commands=
./configure --enable-threads --enable-float
make
make install
the set the enviroment=
setenv CPPFLAGS -I/home/fftw/include
setenv LDFLAGS -L/home/fftw/lib
Then the gromacs installation=
./configure --prefix=/home/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC=mpCC CC=xlC_r -q64 CFLAGS=-O3
-qarch=ppc64 -qtune=auto CXX=xlC_r -q64 CXXFLAGS=-O3 -qarch=ppc64
-qtune=auto F77=mpixlf_r FFLAGS=-O3 -qarch=ppc64 -qtune=auto
the configure did well but while doing make mdrun i started getting
error such as=
source='vmdio.c' object='vmdio.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H
-I. -I../../src -I../../include
-DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3
-qarch=ppc64 -qtune=auto -c -o vmdio.lo vmdio.c
mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3
-qarch=ppc64 -qtune=auto -c vmdio.c -o vmdio.o
1506-503 (W) Option -qlongdouble / -qldbl128 is not supported for
LINUX for Power.
/usr/include/glob.h, line 166.34: 1506-276 (S) Syntax error:
possible missing identifier?
/usr/include/glob.h, line 166.12: 1506-033 (S) Function
__REDIRECT_NTH is not valid. Function cannot return a function.
/usr/include/glob.h, line 166.12: 1506-282 (S) The type of the
parameters must be specified in a prototype.
/usr/include/glob.h, line 169.35: 1506-334 (S) Identifier glob_t has
already been defined on line 113 of /usr/include/glob.h.
/usr/include/glob.h, line 169.42: 1506-277 (S) Syntax error:
possible missing ';' or ','?
/usr/include/glob.h, line 171.39: 1506-276 (S) Syntax error:
possible missing identifier?
/usr/include/glob.h, line 171.13: 1506-282 (S) The type of the
parameters must be specified in a prototype.
/usr/include/glob.h, line 171.13: 1506-343 (S) Redeclaration of
__REDIRECT_NTH differs from previous declaration on line 166 of
/usr/include/glob.h.
/usr/include/glob.h, line 171.13: 1506-050 (I) Return type void in
redeclaration is not compatible with the previous return type
int(const char*,int).
/usr/include/glob.h, line 171.58: 1506-160 (S) Object globfree64
cannot be declared as type void.
/usr/include/glob.h, line 175.12: 1506-343 (S) Redeclaration of
glob64 differs from previous declaration on line 169 of
/usr/include/glob.h.
/usr/include/glob.h, line 175.12: 1506-382 (I) The type int(const
char* restrict,int,int(*)(const char*,int),struct {...}* restrict) of
identifier glob64 differs from previous type int.
make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib make ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/mdlib'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed
by `libmd_mpi.la'. Stop.
make[1]: Leaving directory `/home/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
/bin/sh ../../libtool --tag=CC --mode=link mpCC -O3 -qarch=ppc64
-qtune=auto -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib -o libgmxpreprocess_mpi.la -rpath
/home/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo
gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo
pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo
ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo
topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo
../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
unhandled argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory `/home/gromacs-4.5.5/src/kernel'
please help!
Aiswarya
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Re: [gmx-users] gromacs installation error
You mean that $ ls /home/fftw gives you the content of the installed fftw library (i.e. bin/ include/ lib/ share/)? El 06/12/11 16:21, aiswarya.pa...@gmail.com escribió: Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezoj...@um.es Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS usersgmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs installation error
when i gave following command for gromacs= ./configure --with-fft=fftw3 --enable-float --disable-threads it installed gromacs successfully, but i require a mpi mdrun. when i give enable mpi it gives me same error as fftw3 library not found. Thanks On Wed, Dec 7, 2011 at 2:21 PM, Javier Cerezo j...@um.es wrote: You mean that $ ls /home/fftw gives you the content of the installed fftw library (i.e. bin/ include/ lib/ share/)? El 06/12/11 16:21, aiswarya.pa...@gmail.com escribió: Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezo j...@um.es j...@um.es Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org gmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs installation error
On 7/12/2011 11:25 PM, aiswarya pawar wrote: when i gave following command for gromacs= ./configure --with-fft=fftw3 --enable-float --disable-threads it installed gromacs successfully, but i require a mpi mdrun. when i give enable mpi it gives me same error as fftw3 library not found. Probably something is wrong with (the configuration of) your MPI compiler if it can't pick up the location of FFTW and your normal compiler does. Unfortunately you've made it hard to give any more useful help by losing the original context for the discussion. Mark Thanks On Wed, Dec 7, 2011 at 2:21 PM, Javier Cerezo j...@um.es mailto:j...@um.es wrote: You mean that $ ls /home/fftw gives you the content of the installed fftw library (i.e. bin/ include/ lib/ share/)? El 06/12/11 16:21, aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com escribió: Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezoj...@um.es mailto:j...@um.es Sender:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org mailto:gmx-users@gromacs.org Reply-To: Discussion list for GROMACS usersgmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs installation error
Hi Gromacs users, Am trying to install gromacs-4.5.5 version on IBM cluster with Linux platform and am getting an error such as configure: error: Cannot find fftw3f library. The steps i followed- Installed fftw-3.3 version ./configure --enable-threads --enable-float make make install setenv CPPFLAGS -I/home/fftw/include setenv LDFLAGS -L/home/fftw/lib In gromacs-4.5.5 directory ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3 in this i got the error. please help. Thanks, Aiswarya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs installation error
Are you sure that fftw was installed in /home/fftw? According to the instructions you used to install fftw, it seems that it's been done in the standard location (maybe /usr/local/fftw?), anyway in such a case the system should normally find the libraries without additional CPPFLAGS and LDFLAGS. If not in /home/fftw, try to find where the libraries were installed and change CPPFLAGS and LDFLAGS accordingly (or restart a new session and try without setenv calls) Javier El 06/12/11 10:10, aiswarya pawar escribió: Hi Gromacs users, Am trying to install gromacs-4.5.5 version on IBM cluster with Linux platform and am getting an error such as configure: error: Cannot find fftw3f library. The steps i followed- Installed fftw-3.3 version ./configure --enable-threads --enable-float make make install setenv CPPFLAGS -I/home/fftw/include setenv LDFLAGS -L/home/fftw/lib In gromacs-4.5.5 directory ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3 in this i got the error. please help. Thanks, Aiswarya -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs installation error
Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezo j...@um.es Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8
Dear Gromacs community. I am attempting to install the latest version of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8). I have successfully installed FFTW following the instructions provided on the Gromacs installation page. ./configure --with-fft=fftw3 appears to work properly, but when I perform Make I get the following errors: ld: symbol(s) not found collect2: ld returned 1 exit status make[4]: *** [libgmx.la] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 I did configure my shell (bash) environment, as per the Gromacs installation instructions. Make runs for about 10 minutes before I get these errors. I have searched the mailing list, and have seen people report problems similar to mine, but couldn't determine how those problems were resolved. Also from the mailing list, I understand that the errors I've listed above aren't that informative. If it helps, I repeatedly get the following warnings during Make: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_add_return’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46: warning: implicit declaration of function ‘__sync_add_and_fetch’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_fetch_add’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51: warning: implicit declaration of function ‘__sync_fetch_and_add’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_cas’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57: warning: implicit declaration of function ‘__sync_bool_compare_and_swap’ If anyone has any suggestions, they would be greatly appreciated. Thanks. Matthew Bick Rockefeller University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8
Matthew Bick wrote: Dear Gromacs community. I am attempting to install the latest version of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8). I have successfully installed FFTW following the instructions provided on the Gromacs installation page. ./configure --with-fft=fftw3 appears to work properly, but when I perform Make I get the following errors: ld: symbol(s) not found collect2: ld returned 1 exit status make[4]: *** [libgmx.la] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 The information about the actual missing symbols should be just above this output, so that would be useful information. Also pertinent would be the compiler versions you're using. From what you've posted below it looks like GCC, but which version? I don't think those warnings are particularly harmful, but I know that trying to install a new version of Gromacs on PowerPC can be a challenge. If your compiler is relatively old, you may have to disable some of the newer features, like threading, although that should have been caught during configuration. Is the ./configure command given above the exact command you used? If not, posting that would be useful. -Justin I did configure my shell (bash) environment, as per the Gromacs installation instructions. Make runs for about 10 minutes before I get these errors. I have searched the mailing list, and have seen people report problems similar to mine, but couldn't determine how those problems were resolved. Also from the mailing list, I understand that the errors I've listed above aren't that informative. If it helps, I repeatedly get the following warnings during Make: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_add_return’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46: warning: implicit declaration of function ‘__sync_add_and_fetch’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_fetch_add’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51: warning: implicit declaration of function ‘__sync_fetch_and_add’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_cas’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57: warning: implicit declaration of function ‘__sync_bool_compare_and_swap’ If anyone has any suggestions, they would be greatly appreciated. Thanks. Matthew Bick Rockefeller University -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8
On 2011-05-23 02:37:54PM -0500, Matthew Bick wrote: Dear Gromacs community. I am attempting to install the latest version of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8). I have successfully installed FFTW following the instructions provided on the Gromacs installation page. ./configure --with-fft=fftw3 appears to work properly, but when I perform Make I get the following errors: ld: symbol(s) not found collect2: ld returned 1 exit status make[4]: *** [libgmx.la] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 I did configure my shell (bash) environment, as per the Gromacs installation instructions. Make runs for about 10 minutes before I get these errors. I have searched the mailing list, and have seen people report problems similar to mine, but couldn't determine how those problems were resolved. Also from the mailing list, I understand that the errors I've listed above aren't that informative. If it helps, I repeatedly get the following warnings during Make: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_add_return’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46: warning: implicit declaration of function ‘__sync_add_and_fetch’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_fetch_add’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51: warning: implicit declaration of function ‘__sync_fetch_and_add’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_cas’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57: warning: implicit declaration of function ‘__sync_bool_compare_and_swap’ If anyone has any suggestions, they would be greatly appreciated. Thanks. Some things to watch out for: single vs. double precision (the library versions must match between fftw and what you passed to ./configure for gromacs (--enable-float is single precision,--disable-float is double). Maybe you need --enable-shared and specify correct LDFLAGS... The warnings section seems to imply this is happening in the threads/MPI section, Justin can correct me if I'm wrong, but maybe you need to explicitly disable mpi with --disable-mpi in the configure? Gromacs 4.5.4 is also in MacPorts, which contains a simplified options framework (and will install gcc45 for you if you want as well) for all the popular configure variations: http://www.macports.org/ports.php?by=namesubstr=gromacs (I would probably go with +gcc45, +gsl, +no_x11 [avoids openmotif] and +optimize [for gsl]) Once you do get it working, watchout for overheating on that thing :) -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8
Peter C. Lai wrote: On 2011-05-23 02:37:54PM -0500, Matthew Bick wrote: Dear Gromacs community. I am attempting to install the latest version of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8). I have successfully installed FFTW following the instructions provided on the Gromacs installation page. ./configure --with-fft=fftw3 appears to work properly, but when I perform Make I get the following errors: ld: symbol(s) not found collect2: ld returned 1 exit status make[4]: *** [libgmx.la] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 I did configure my shell (bash) environment, as per the Gromacs installation instructions. Make runs for about 10 minutes before I get these errors. I have searched the mailing list, and have seen people report problems similar to mine, but couldn't determine how those problems were resolved. Also from the mailing list, I understand that the errors I've listed above aren't that informative. If it helps, I repeatedly get the following warnings during Make: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_add_return’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46: warning: implicit declaration of function ‘__sync_add_and_fetch’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_fetch_add’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51: warning: implicit declaration of function ‘__sync_fetch_and_add’ ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In function ‘tMPI_Atomic_cas’: ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57: warning: implicit declaration of function ‘__sync_bool_compare_and_swap’ If anyone has any suggestions, they would be greatly appreciated. Thanks. Some things to watch out for: single vs. double precision (the library versions must match between fftw and what you passed to ./configure for gromacs (--enable-float is single precision,--disable-float is double). If incorrect FFTW libraries were found, configuration would have failed. Maybe you need --enable-shared and specify correct LDFLAGS... The warnings section seems to imply this is happening in the threads/MPI section, Justin can correct me if I'm wrong, but maybe you need to explicitly disable mpi with --disable-mpi in the configure? The thread_mpi library corresponds to the internal threading built into Gromacs and doesn't have anything to do with external MPI libraries. The --disable-mpi option is the default behavior, anyway, and is only used in case of an MPI (non-threading) build. It is worth noting that in a single installation step, threading and MPI cannot be mixed; you use one or the other. A full configuration command would be necessary to see what's going on. -Justin Gromacs 4.5.4 is also in MacPorts, which contains a simplified options framework (and will install gcc45 for you if you want as well) for all the popular configure variations: http://www.macports.org/ports.php?by=namesubstr=gromacs (I would probably go with +gcc45, +gsl, +no_x11 [avoids openmotif] and +optimize [for gsl]) Once you do get it working, watchout for overheating on that thing :) -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
