Re: [votca] Re: Error after re-installation of VOTCA
Hi,
that is why I would use a shared version of libgmx (libgmx.so),
all these 'undefined reference' below are coming from libraries libgmx
depends on, e.g. libm, libpthreads and libdl. So either you add libm
and libthreads to GROMACS_DEP_LIBRARIES (like the error message
suggests) or just recompile gromacs with --enable-shared when using
configure.
You could also build gromacs using build.sh, then it is shared by
default as it uses gromacs' cmake files.
Cheers,
Christoph
Am 12. Oktober 2011 12:24 schrieb Patrick Kiley pjki...@gmail.com:
Hi Christoph,
I think I have made more progress, but am still getting stuck. I deleted
the whole directory and started over. This time I compiled VOTCA this way:
./build.sh --prefix ${prefix} -DGMX_DOUBLE=ON tools csg
The result was that it found libgmx_d this time. However, it died with this
error:
-- checking for module 'libgmx_d'
-- found libgmx_d, version 4.5.4
-- Looking for GromacsVersion in /usr/local/gromacs/lib/libgmx_d.a;
-- Looking for GromacsVersion in /usr/local/gromacs/lib/libgmx_d.a; - not
found
CMake Error at CMakeModules/FindGROMACS.cmake:81 (message):
Could not find GromacsVersion in /usr/local/gromacs/lib/libgmx_d.a;, take
look at the error message in
/home/patrick/votca/src/csg/CMakeFiles/CMakeError.log to find out what was
going wrong. If you don't have pkg-config installed you will most likely
have to set GROMACS_LIBRARY and GROMACS_DEP_LIBRARY by hand which sets the
gromacs lib and it's depencies (i.e.
-DGROMACS_LIBRARY='/path/to/libgmx.so'
-DGROMACS_DEP_LIBRARIES='/path/to/libblas.so;/path/to/libm.so') !
Call Stack (most recent call first):
src/libcsg/CMakeLists.txt:23 (find_package)
Here is the contents of
/home/patrick/votca/src/csg/CMakeFiles/CMakeError.log:
Determining if the function GromacsVersion exists in the
/usr/local/gromacs/lib/libgmx_d.a; failed with the following output:
Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/make cmTryCompileExec/fast
/usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
CMakeFiles/cmTryCompileExec.dir/build
make[1]: Entering directory
`/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp'
/usr/local/bin/cmake -E cmake_progress_report
/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o
/usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o
CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c
/usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec
/usr/local/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
/usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion
CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec
-rdynamic /usr/local/gromacs/lib/libgmx_d.a
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_key_delete':
pthreads.c:(.text+0x619): undefined reference to `pthread_key_delete'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_key_create':
pthreads.c:(.text+0x68e): undefined reference to `pthread_key_create'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_join':
pthreads.c:(.text+0x800): undefined reference to `pthread_join'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_create':
pthreads.c:(.text+0x87a): undefined reference to `pthread_create'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_cancel':
pthreads.c:(.text+0x174): undefined reference to `pthread_cancel'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_setspecific':
pthreads.c:(.text+0x1ff): undefined reference to `pthread_setspecific'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_getspecific':
pthreads.c:(.text+0x21c): undefined reference to `pthread_getspecific'
/usr/local/gromacs/lib/libgmx_d.a(pthreads.c.o): In function
`tMPI_Thread_mutex_trylock':
pthreads.c:(.text+0x925): undefined reference to `pthread_mutex_trylock'
/usr/local/gromacs/lib/libgmx_d.a(pbc.c.o): In function `low_set_pbc':
pbc.c:(.text+0x71a0): undefined reference to `sqrt'
pbc.c:(.text+0x7763): undefined reference to `sqrt'
pbc.c:(.text+0x7800): undefined reference to `sqrt'
/usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `dopdihs':
bondfree.c:(.text+0x780): undefined reference to `sincos'
/usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `FENE_bonds':
bondfree.c:(.text+0x2256): undefined reference to `log'
/usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `morse_bonds':
bondfree.c:(.text+0x2d83): undefined reference to `exp'
/usr/local/gromacs/lib/libgmx_d.a(bondfree.c.o): In function `low_angres':
bondfree.c:(.text+0x58a2): undefined reference to `acos'
bondfree.c:(.text+0x5973): undefined reference to `sincos'
Re: [votca] Re: Error after re-installation of VOTCA
Just as a side note: build.sh can also build and install gromacs. $ ./build.sh gromacs Patrick, I guess you have a non-standard version of gromacs, right? So just run: $ ./build.sh -U gromacs and then overwrite the gromacs directory with your own gromacs version and execute $ ./build.sh gromacs Possibly you have to add the --clean option to the build.sh command line. Cheers, Christoph Am 11. Oktober 2011 14:12 schrieb Valentina valentina_erast...@yahoo.co.uk: Oh, sorry, I read topol.tpr at the beginning. I had a similar problem before. This may be useful? http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9 Valentina On Oct 11, 12:52 pm, Patrick Kiley pjki...@gmail.com wrote: I seem to remember that there used to be a --conf-opts option for build.sh that enabled me to build static libs. Does this still exist? I just tried using it, but it doesn't seem to be recognized. Patrick On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley pjki...@gmail.com wrote: Dear all, Sorry, that was a mistake on my part. I am actually using the .tpr files. The command was: csg_boltzmann --top topol.tpr --cg map5-gly-pro-pro.xml --excl --trj traj.trr sorry for the confusion. Patrick On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch frit...@mpip-mainz.mpg.de wrote: Hello Patrick, you need to use the topol.tpr which is the binary form of the topol.top. To get the .tpr you have to run the gromacs preprocessor (grompp). -Sebastian Dear all, I have recently recompiled GROMACS on my machine, and therefore have needed to recompile VOTCA. Here is how I did it: 1) source gromacs 2) sudo ./build.sh -R -dcu --release 1.2.1 --prefix=/home/votca/ tools csg This finishes with no errors, so I thought everything should be OK. However, when I run this command: csg_boltzmann --top topol.top --cg map.xml --excl --trj traj.trr I get this error: an error occurred: input format not supported: topol.top To me this means I have somehow compiled without GMX support, but how could this be and how can I fix it? One other thing, I have compiled gromacs with static libs, so maybe I need to tell the build script this explicitly? Thanks for any help you can give, Patrick Kiley -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- Christoph Junghans Votca Core Developer Web: http://www.votca.org -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
Re: [votca] Re: Error after re-installation of VOTCA
Hi Valentina, Thanks for the link, but unfortunately, I get zero errors during compilation, so I think this case is a little different from yours, but someone please correct me if I am wrong. Patrick On Tue, Oct 11, 2011 at 1:12 PM, Valentina valentina_erast...@yahoo.co.ukwrote: Oh, sorry, I read topol.tpr at the beginning. I had a similar problem before. This may be useful? http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9 Valentina On Oct 11, 12:52 pm, Patrick Kiley pjki...@gmail.com wrote: I seem to remember that there used to be a --conf-opts option for build.sh that enabled me to build static libs. Does this still exist? I just tried using it, but it doesn't seem to be recognized. Patrick On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley pjki...@gmail.com wrote: Dear all, Sorry, that was a mistake on my part. I am actually using the .tpr files. The command was: csg_boltzmann --top topol.tpr --cg map5-gly-pro-pro.xml --excl --trj traj.trr sorry for the confusion. Patrick On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch frit...@mpip-mainz.mpg.de wrote: Hello Patrick, you need to use the topol.tpr which is the binary form of the topol.top. To get the .tpr you have to run the gromacs preprocessor (grompp). -Sebastian Dear all, I have recently recompiled GROMACS on my machine, and therefore have needed to recompile VOTCA. Here is how I did it: 1) source gromacs 2) sudo ./build.sh -R -dcu --release 1.2.1 --prefix=/home/votca/ tools csg This finishes with no errors, so I thought everything should be OK. However, when I run this command: csg_boltzmann --top topol.top --cg map.xml --excl --trj traj.trr I get this error: an error occurred: input format not supported: topol.top To me this means I have somehow compiled without GMX support, but how could this be and how can I fix it? One other thing, I have compiled gromacs with static libs, so maybe I need to tell the build script this explicitly? Thanks for any help you can give, Patrick Kiley -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
Re: [votca] Re: Error after re-installation of VOTCA
Hi Christoph, I tried your suggestion, but it doesn't work. I get this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. I tried a fresh install of the normal gromacs compiled as static, and tried recompiling votca against it and finally I get this error: -- package 'libgmx_d' not found -- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR) CMake Warning at src/libcsg/CMakeLists.txt:41 (message): gromacs-4.5 double precision not found failback to single precision -- checking for module 'libgmx' -- package 'libgmx' not found -- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR) CMake Error at src/libcsg/CMakeLists.txt:44 (message): gromacs-4.5 (single or double) not found, make sure you have installed the gromacs-4.5 and it's dev package. If the gromacs module was not found above, make sure you have sourced GMXRC or set PKG_CONFIG_PATH yourself. gromacs support can be disable it with -DWITH_GMX=OFF. If you have gromacs-5.0 installed enable to build against it with -DWITH_GMX_DEVEL=ON -- Configuring incomplete, errors occurred! According to Valentina's link: echo $PKG_CONFIG_PATH produces: /usr/local/gromacs/lib/pkgconfig which I believe is correct. Any other ideas? Kind regards, Patrick On Tue, Oct 11, 2011 at 1:23 PM, Patrick Kiley pjki...@gmail.com wrote: Hi Valentina, Thanks for the link, but unfortunately, I get zero errors during compilation, so I think this case is a little different from yours, but someone please correct me if I am wrong. Patrick On Tue, Oct 11, 2011 at 1:12 PM, Valentina valentina_erast...@yahoo.co.uk wrote: Oh, sorry, I read topol.tpr at the beginning. I had a similar problem before. This may be useful? http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9 Valentina On Oct 11, 12:52 pm, Patrick Kiley pjki...@gmail.com wrote: I seem to remember that there used to be a --conf-opts option for build.sh that enabled me to build static libs. Does this still exist? I just tried using it, but it doesn't seem to be recognized. Patrick On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley pjki...@gmail.com wrote: Dear all, Sorry, that was a mistake on my part. I am actually using the .tpr files. The command was: csg_boltzmann --top topol.tpr --cg map5-gly-pro-pro.xml --excl --trj traj.trr sorry for the confusion. Patrick On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch frit...@mpip-mainz.mpg.de wrote: Hello Patrick, you need to use the topol.tpr which is the binary form of the topol.top. To get the .tpr you have to run the gromacs preprocessor (grompp). -Sebastian Dear all, I have recently recompiled GROMACS on my machine, and therefore have needed to recompile VOTCA. Here is how I did it: 1) source gromacs 2) sudo ./build.sh -R -dcu --release 1.2.1 --prefix=/home/votca/ tools csg This finishes with no errors, so I thought everything should be OK. However, when I run this command: csg_boltzmann --top topol.top --cg map.xml --excl --trj traj.trr I get this error: an error occurred: input format not supported: topol.top To me this means I have somehow compiled without GMX support, but how could this be and how can I fix it? One other thing, I have compiled gromacs with static libs, so maybe I need to tell the build script this explicitly? Thanks for any help you can give, Patrick Kiley -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
Re: [votca] Re: Error after re-installation of VOTCA
Am 11. Oktober 2011 16:24 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, I tried your suggestion, but it doesn't work. I get this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. Hmm, that could be the fPIC bug of gcc, but this looks more like a mixture of 64 and 32 bit libraries. Are all dependence libraries (gsl, fftw, libgmx ...) are compiled in 64bit? e.g. $ file ~/votca/lib/libgmx.so.6 libgmx.so.6: ELF 64-bit LSB shared object, x86-64 I tried a fresh install of the normal gromacs compiled as static, and tried Well, I hope you have a good reason to go through the pain of compiling statically! Even the gromacs people now compile shared by default. In case you still want to do it, here is a thread with hints: https://groups.google.com/group/votca/browse_thread/thread/c4a847aabfa5f643/054959940df46f recompiling votca against it and finally I get this error: -- package 'libgmx_d' not found -- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR) CMake Warning at src/libcsg/CMakeLists.txt:41 (message): gromacs-4.5 double precision not found failback to single precision -- checking for module 'libgmx' -- package 'libgmx' not found -- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR) CMake Error at src/libcsg/CMakeLists.txt:44 (message): gromacs-4.5 (single or double) not found, make sure you have installed the gromacs-4.5 and it's dev package. If the gromacs module was not found above, make sure you have sourced GMXRC or set PKG_CONFIG_PATH yourself. gromacs support can be disable it with -DWITH_GMX=OFF. If you have gromacs-5.0 installed enable to build against it with -DWITH_GMX_DEVEL=ON -- Configuring incomplete, errors occurred! According to Valentina's link: echo $PKG_CONFIG_PATH produces: /usr/local/gromacs/lib/pkgconfig which I believe is correct. Can you post the output of $ pkg-config --libs libgmx Cheers, Christoph Any other ideas? Kind regards, Patrick On Tue, Oct 11, 2011 at 1:23 PM, Patrick Kiley pjki...@gmail.com wrote: Hi Valentina, Thanks for the link, but unfortunately, I get zero errors during compilation, so I think this case is a little different from yours, but someone please correct me if I am wrong. Patrick On Tue, Oct 11, 2011 at 1:12 PM, Valentina valentina_erast...@yahoo.co.uk wrote: Oh, sorry, I read topol.tpr at the beginning. I had a similar problem before. This may be useful? http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9 Valentina On Oct 11, 12:52 pm, Patrick Kiley pjki...@gmail.com wrote: I seem to remember that there used to be a --conf-opts option for build.sh that enabled me to build static libs. Does this still exist? I just tried using it, but it doesn't seem to be recognized. Patrick On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley pjki...@gmail.com wrote: Dear all, Sorry, that was a mistake on my part. I am actually using the .tpr files. The command was: csg_boltzmann --top topol.tpr --cg map5-gly-pro-pro.xml --excl --trj traj.trr sorry for the confusion. Patrick On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch frit...@mpip-mainz.mpg.de wrote: Hello Patrick, you need to use the topol.tpr which is the binary form of the topol.top. To get the .tpr you have to run the gromacs preprocessor (grompp). -Sebastian Dear all, I have recently recompiled GROMACS on my machine, and therefore have needed to recompile VOTCA. Here is how I did it: 1) source gromacs 2) sudo ./build.sh -R -dcu --release 1.2.1 --prefix=/home/votca/ tools csg This finishes with no errors, so I thought everything should be OK. However, when I run this command: csg_boltzmann --top topol.top --cg map.xml --excl --trj traj.trr I get this error: an error occurred: input format not supported: topol.top To me this means I have somehow compiled without GMX support, but how could this be and how can I fix it? One other thing, I have compiled gromacs with static libs, so maybe I need to tell the build script this explicitly? Thanks for any help you can give, Patrick Kiley -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at
Re: [votca] Re: Error after re-installation of VOTCA
Hi Christoph, Here is the output of $ pkg-config --libs libgmx: Package libgmx was not found in the pkg-config search path. Perhaps you should add the directory containing `libgmx.pc' to the PKG_CONFIG_PATH environment variable No package 'libgmx' found On Tue, Oct 11, 2011 at 3:45 PM, Christoph Junghans jungh...@votca.orgwrote: Am 11. Oktober 2011 16:24 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, I tried your suggestion, but it doesn't work. I get this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. Hmm, that could be the fPIC bug of gcc, but this looks more like a mixture of 64 and 32 bit libraries. Are all dependence libraries (gsl, fftw, libgmx ...) are compiled in 64bit? e.g. $ file ~/votca/lib/libgmx.so.6 libgmx.so.6: ELF 64-bit LSB shared object, x86-64 I tried a fresh install of the normal gromacs compiled as static, and tried Well, I hope you have a good reason to go through the pain of compiling statically! Even the gromacs people now compile shared by default. In case you still want to do it, here is a thread with hints: https://groups.google.com/group/votca/browse_thread/thread/c4a847aabfa5f643/054959940df46f recompiling votca against it and finally I get this error: -- package 'libgmx_d' not found -- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR) CMake Warning at src/libcsg/CMakeLists.txt:41 (message): gromacs-4.5 double precision not found failback to single precision -- checking for module 'libgmx' -- package 'libgmx' not found -- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR) CMake Error at src/libcsg/CMakeLists.txt:44 (message): gromacs-4.5 (single or double) not found, make sure you have installed the gromacs-4.5 and it's dev package. If the gromacs module was not found above, make sure you have sourced GMXRC or set PKG_CONFIG_PATH yourself. gromacs support can be disable it with -DWITH_GMX=OFF. If you have gromacs-5.0 installed enable to build against it with -DWITH_GMX_DEVEL=ON -- Configuring incomplete, errors occurred! According to Valentina's link: echo $PKG_CONFIG_PATH produces: /usr/local/gromacs/lib/pkgconfig which I believe is correct. Can you post the output of $ pkg-config --libs libgmx Cheers, Christoph Any other ideas? Kind regards, Patrick On Tue, Oct 11, 2011 at 1:23 PM, Patrick Kiley pjki...@gmail.com wrote: Hi Valentina, Thanks for the link, but unfortunately, I get zero errors during compilation, so I think this case is a little different from yours, but someone please correct me if I am wrong. Patrick On Tue, Oct 11, 2011 at 1:12 PM, Valentina valentina_erast...@yahoo.co.uk wrote: Oh, sorry, I read topol.tpr at the beginning. I had a similar problem before. This may be useful? http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9 Valentina On Oct 11, 12:52 pm, Patrick Kiley pjki...@gmail.com wrote: I seem to remember that there used to be a --conf-opts option for build.sh that enabled me to build static libs. Does this still exist? I just tried using it, but it doesn't seem to be recognized. Patrick On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley pjki...@gmail.com wrote: Dear all, Sorry, that was a mistake on my part. I am actually using the .tpr files. The command was: csg_boltzmann --top topol.tpr --cg map5-gly-pro-pro.xml --excl --trj traj.trr sorry for the confusion. Patrick On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch frit...@mpip-mainz.mpg.de wrote: Hello Patrick, you need to use the topol.tpr which is the binary form of the topol.top. To get the .tpr you have to run the gromacs preprocessor (grompp). -Sebastian Dear all, I have recently recompiled GROMACS on my machine, and therefore have needed to recompile VOTCA. Here is how I did it: 1) source gromacs 2) sudo ./build.sh -R -dcu --release 1.2.1 --prefix=/home/votca/ tools csg This finishes with no errors, so I thought everything should be OK. However, when I run this command: csg_boltzmann --top topol.top --cg map.xml --excl --trj traj.trr I get this error: an error occurred: input format not supported: topol.top To me this means I have somehow compiled without GMX support, but how could this be and how can I fix it? One other thing, I have compiled gromacs with static libs, so maybe I need to tell the build script this explicitly? Thanks for any help you can give, Patrick Kiley -- You received this message because you are subscribed to the Google Groups votca group. To post to this group, send email to
Re: [votca] Re: Error after re-installation of VOTCA
Here is the contents of the entire file: Determining if the function GromacsVersion exists in the /usr/local/gromacs/lib/libgmx.a failed with the following output: Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make cmTryCompileExec/fast /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build make[1]: Entering directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' /usr/local/bin/cmake -E cmake_progress_report /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c make[1]: Leaving directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' make[1]: *** No rule to make target `/usr/local/gromacs/lib/libgmx.a', needed by `cmTryCompileExec'. Stop. make: *** [cmTryCompileExec/fast] Error 2 Determining if the function GromacsVersion exists in the /usr/local/gromacs/lib failed with the following output: Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make cmTryCompileExec/fast /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build make[1]: Entering directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' /usr/local/bin/cmake -E cmake_progress_report /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c Linking C executable cmTryCompileExec /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1 /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -rdynamic CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o: In function `main': CheckFunctionExists.c:(.text+0x15): undefined reference to `GromacsVersion' collect2: ld returned 1 exit status make[1]: Leaving directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' make[1]: *** [cmTryCompileExec] Error 1 make: *** [cmTryCompileExec/fast] Error 2 On Tue, Oct 11, 2011 at 5:02 PM, Christoph Junghans jungh...@votca.orgwrote: Am 11. Oktober 2011 17:40 schrieb Patrick Kiley pjki...@gmail.com: Sorry! I should have realized that was what you were asking $ pkg-config --libs libgmx_d produces: -L/usr/local/gromacs/lib -lgmx_d That looks ok to me, but it doesn't fit with -- package 'libgmx_d' not found From your email above. What kind of error does csg/CMakeFiles/CMakeError.log report at the end? Christoph Patrick On Tue, Oct 11, 2011 at 4:24 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 17:05 schrieb Patrick Kiley pjki...@gmail.com: I have definitely sourced gromacs. So many times . . . Here is the output of ls /usr/local/gromacs/lib/pkgconfig/: libgmxana_d.pc libgmx_d.pc libgmxpreprocess_d.pc libmd_d.pc Ah ok, so what is the output of $ pkg-config --libs libgmx_d then? On Tue, Oct 11, 2011 at 3:57 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 16:50 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, Here is the output of $ pkg-config --libs libgmx: Package libgmx was not found in the pkg-config search path. Perhaps you should add the directory containing `libgmx.pc' to the PKG_CONFIG_PATH environment variable No package 'libgmx' found what does contain /usr/local/gromacs/lib/pkgconfig then? Have you sourced GMXRC? Cheers, Christoph On Tue, Oct 11, 2011 at 3:45 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 16:24 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, I tried your suggestion, but it doesn't work. I get this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. Hmm, that could be the fPIC bug of gcc, but this looks more like a mixture of 64 and 32 bit libraries. Are all dependence libraries (gsl, fftw, libgmx ...) are compiled in 64bit? e.g. $ file ~/votca/lib/libgmx.so.6 libgmx.so.6: ELF 64-bit LSB shared object, x86-64 I tried a fresh install of the normal gromacs compiled as static, and tried Well, I hope you have a good reason to go through the pain of compiling statically! Even the gromacs people now compile shared by default. In case you still want to do it, here is a thread with hints:
Re: [votca] Re: Error after re-installation of VOTCA
Am 11. Oktober 2011 18:08 schrieb Patrick Kiley pjki...@gmail.com: Here is the contents of the entire file: Determining if the function GromacsVersion exists in the /usr/local/gromacs/lib failed with the following output: That looks strange to me, did you specify GMX_LIBRARY by hand? For very odd systems you can specify all libs by hand, for examples see the build.sh line in https://code.google.com/p/votca/wiki/compiling_AIX Christoph Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make cmTryCompileExec/fast /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build make[1]: Entering directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' /usr/local/bin/cmake -E cmake_progress_report /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c Linking C executable cmTryCompileExec /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1 /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -rdynamic CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o: In function `main': CheckFunctionExists.c:(.text+0x15): undefined reference to `GromacsVersion' collect2: ld returned 1 exit status make[1]: Leaving directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' make[1]: *** [cmTryCompileExec] Error 1 make: *** [cmTryCompileExec/fast] Error 2 On Tue, Oct 11, 2011 at 5:02 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 17:40 schrieb Patrick Kiley pjki...@gmail.com: Sorry! I should have realized that was what you were asking $ pkg-config --libs libgmx_d produces: -L/usr/local/gromacs/lib -lgmx_d That looks ok to me, but it doesn't fit with -- package 'libgmx_d' not found From your email above. What kind of error does csg/CMakeFiles/CMakeError.log report at the end? Christoph Patrick On Tue, Oct 11, 2011 at 4:24 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 17:05 schrieb Patrick Kiley pjki...@gmail.com: I have definitely sourced gromacs. So many times . . . Here is the output of ls /usr/local/gromacs/lib/pkgconfig/: libgmxana_d.pc libgmx_d.pc libgmxpreprocess_d.pc libmd_d.pc Ah ok, so what is the output of $ pkg-config --libs libgmx_d then? On Tue, Oct 11, 2011 at 3:57 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 16:50 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, Here is the output of $ pkg-config --libs libgmx: Package libgmx was not found in the pkg-config search path. Perhaps you should add the directory containing `libgmx.pc' to the PKG_CONFIG_PATH environment variable No package 'libgmx' found what does contain /usr/local/gromacs/lib/pkgconfig then? Have you sourced GMXRC? Cheers, Christoph On Tue, Oct 11, 2011 at 3:45 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 16:24 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, I tried your suggestion, but it doesn't work. I get this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. Hmm, that could be the fPIC bug of gcc, but this looks more like a mixture of 64 and 32 bit libraries. Are all dependence libraries (gsl, fftw, libgmx ...) are compiled in 64bit? e.g. $ file ~/votca/lib/libgmx.so.6 libgmx.so.6: ELF 64-bit LSB shared object, x86-64 I tried a fresh install of the normal gromacs compiled as static, and tried Well, I hope you have a good reason to go through the pain of compiling statically! Even the gromacs people now compile shared by default. In case you still want to do it, here is a thread with hints: https://groups.google.com/group/votca/browse_thread/thread/c4a847aabfa5f643/054959940df46f recompiling votca against it and finally I get this error: -- package 'libgmx_d' not found -- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR) CMake Warning at src/libcsg/CMakeLists.txt:41 (message): gromacs-4.5 double precision not found failback to single precision -- checking for module 'libgmx' -- package 'libgmx' not found -- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR) CMake Error at src/libcsg/CMakeLists.txt:44 (message): gromacs-4.5 (single or double) not found, make sure you
Re: [votca] Re: Error after re-installation of VOTCA
I didn't specify anything by hand in the case above. Since I am using double precision gmx, should I specify -DGMX_D_LIBRARY rather than _DGMX_LIBRARY? patrick On Tue, Oct 11, 2011 at 5:17 PM, Christoph Junghans jungh...@votca.orgwrote: Am 11. Oktober 2011 18:08 schrieb Patrick Kiley pjki...@gmail.com: Here is the contents of the entire file: Determining if the function GromacsVersion exists in the /usr/local/gromacs/lib failed with the following output: That looks strange to me, did you specify GMX_LIBRARY by hand? For very odd systems you can specify all libs by hand, for examples see the build.sh line in https://code.google.com/p/votca/wiki/compiling_AIX Christoph Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/make cmTryCompileExec/fast /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build make[1]: Entering directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' /usr/local/bin/cmake -E cmake_progress_report /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c Linking C executable cmTryCompileExec /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1 /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -rdynamic CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o: In function `main': CheckFunctionExists.c:(.text+0x15): undefined reference to `GromacsVersion' collect2: ld returned 1 exit status make[1]: Leaving directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' make[1]: *** [cmTryCompileExec] Error 1 make: *** [cmTryCompileExec/fast] Error 2 On Tue, Oct 11, 2011 at 5:02 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 17:40 schrieb Patrick Kiley pjki...@gmail.com: Sorry! I should have realized that was what you were asking $ pkg-config --libs libgmx_d produces: -L/usr/local/gromacs/lib -lgmx_d That looks ok to me, but it doesn't fit with -- package 'libgmx_d' not found From your email above. What kind of error does csg/CMakeFiles/CMakeError.log report at the end? Christoph Patrick On Tue, Oct 11, 2011 at 4:24 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 17:05 schrieb Patrick Kiley pjki...@gmail.com: I have definitely sourced gromacs. So many times . . . Here is the output of ls /usr/local/gromacs/lib/pkgconfig/: libgmxana_d.pc libgmx_d.pc libgmxpreprocess_d.pc libmd_d.pc Ah ok, so what is the output of $ pkg-config --libs libgmx_d then? On Tue, Oct 11, 2011 at 3:57 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 16:50 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, Here is the output of $ pkg-config --libs libgmx: Package libgmx was not found in the pkg-config search path. Perhaps you should add the directory containing `libgmx.pc' to the PKG_CONFIG_PATH environment variable No package 'libgmx' found what does contain /usr/local/gromacs/lib/pkgconfig then? Have you sourced GMXRC? Cheers, Christoph On Tue, Oct 11, 2011 at 3:45 PM, Christoph Junghans jungh...@votca.org wrote: Am 11. Oktober 2011 16:24 schrieb Patrick Kiley pjki...@gmail.com: Hi Christoph, I tried your suggestion, but it doesn't work. I get this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. Hmm, that could be the fPIC bug of gcc, but this looks more like a mixture of 64 and 32 bit libraries. Are all dependence libraries (gsl, fftw, libgmx ...) are compiled in 64bit? e.g. $ file ~/votca/lib/libgmx.so.6 libgmx.so.6: ELF 64-bit LSB shared object, x86-64 I tried a fresh install of the normal gromacs compiled as static, and tried Well, I hope you have a good reason to go through the pain of compiling statically! Even the gromacs people now compile shared by default. In case you still want to do it, here is a thread with hints: https://groups.google.com/group/votca/browse_thread/thread/c4a847aabfa5f643/054959940df46f recompiling votca against it and finally I get this error: -- package 'libgmx_d' not found -- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR) CMake Warning
