Re: [gmx-users] problem compiling gromacs 5.1

HI, I was able to compile gromacs 5.1 via: cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include" -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_DOUBLE=OFF

[gmx-users] problem compiling gromacs 5.1

HI, I tried to configure gromacs 5.1 via: ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a

Re: [gmx-users] problem compiling gromacs 5.1

Hi, That one's our fault, sorry :-( It'll be fixed in 5.1.1 out shortly, but you can work around it by adding -DSPHINX_EXECUTABLE=no to your cmake call (which, by the way, still has a lot of stuff in it that I've said you don't want to have) Mark On Sat, Oct 24, 2015 at 6:14 PM Ana Marija

Re: [gmx-users] problem compiling gromacs 5.1

so I managed to install gromacs via: #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a

Re: [gmx-users] problem compiling gromacs 5.1

Hi, On Sat, Oct 24, 2015 at 8:22 PM Ana Marija wrote: > so I managed to install gromacs via: > > #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> > > cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include >

Re: [gmx-users] problem compiling gromacs 5.1

For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5. What I am asking here is not weather my admins are doing a good job,and also as you know some things you just got with machine,and sometimes things are not great,so you have to make a workaround. What I am asking here is what

Re: [gmx-users] problem compiling gromacs 5.1

Hi, The purpose of using a wrapper compiler is that it handles linking all the right stuff. MPI_LIBRARY was a thing from a cmake module we used only in Gromacs 4.5, before we removed it when we decided that wrapper compilers do a better job. So there's nothing that replaces it. That the recent

Re: [gmx-users] Problem compiling Gromacs 5.1

Thanks, Mark. I inserted quotation in line 52 as Mark suggested. I tried cmake again and got the only error. Boost = 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against GROMACS. I don't know what the

Re: [gmx-users] Problem compiling Gromacs 5.1

On 8/21/15 11:18 AM, Atsutoshi Okabe wrote: Thanks, Mark. I inserted quotation in line 52 as Mark suggested. I tried cmake again and got the only error. Boost = 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses

Re: [gmx-users] Problem compiling Gromacs 5.1

Thanks, Peter. But , I mean I don’t know what line I should change to from line 52 of cmake/FindPhinx.cmake to solve this error. Leucer 2015/08/20 16:02、Kroon, P.C. p.c.kr...@rug.nl のメール： Just use your favourite text editor. Peter On Thu, Aug 20, 2015 at 3:10 AM,

Re: [gmx-users] Problem compiling Gromacs 5.1

Hi, You should change line 52 from what it is, to what I suggested - which inserts quotation marks around one of the variable interpolations. Mark On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 atsutoshi0...@gmail.com wrote: Thanks, Peter. But , I mean I don’t know what line I should change to from

Re: [gmx-users] Problem compiling Gromacs 5.1

On 8/20/15 8:42 AM, 岡部篤俊 wrote: Thanks, Peter. But , I mean I don’t know what line I should change to from line 52 of cmake/FindPhinx.cmake to solve this error. Mark's message provided the corrected line. Just replace whatever is on line 52 with that. -Justin Leucer 2015/08/20

Re: [gmx-users] Problem compiling Gromacs 5.1

Just use your favourite text editor. Peter On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote: Line 52 of cmake/FindSphinx.cmake file is written below. string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1 SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE}) Can you tell

[gmx-users] Problem compiling Gromacs 5.1

Hi, I am unable to compile Gromamcs 5.1 using the following cmake command. cmake .. -DGMX_FFT_LIBRARY=fftpack -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1 -DGMX_USE_RDTSCP=off Then I got the error message. Boost =

Re: [gmx-users] Problem compiling Gromacs 5.1

Hi, As the error says you should get a version =1.44 for the boost libraries On 19/08/15 15:49, 岡部篤俊 wrote: g minimal internal version. T -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133

Re: [gmx-users] Problem compiling Gromacs 5.1

Hi, On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote: Hi, I am unable to compile Gromamcs 5.1 using the following cmake command. cmake .. -DGMX_FFT_LIBRARY=fftpack -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off -DGMX_THREAD_MPI=off -DGMX_MPI=on

Re: [gmx-users] Problem compiling Gromacs 5.1

Yeah sorry, I realized later that I did not read the complete thing... Bad habit. On 19/08/15 16:18, Mark Abraham wrote: Hi, No, the warning about Boost versions is unrelated and just happens to precede the issue. Mark On Wed, Aug 19, 2015 at 4:13 PM Felipe Merino

Re: [gmx-users] Problem compiling Gromacs 5.1

Line 52 of cmake/FindSphinx.cmake file is written below. string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1 SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE}) Can you tell me how I can change the line? Bests, Leucer 2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:

[gmx-users] Problem compiling Gromacs 5.1 with XL Compiler

Hi, I am unable to compile Gromacs 5.1 using the XL compiler (version 12.1.0) on our BlueGene/Q cluster. Before starting I set the relevant paths like so: export PATH=/bgsys/drivers/ppcfloor/comm/xl/bin/:$PATH export LD_LIBRARY_PATH=/bgsys/drivers/ppcfloor/comm/xl/lib/:$LD_LIBRARY_PATH export

Re: [gmx-users] Problem compiling Gromacs 5.1 with XL Compiler

Hi, That all seems wildly unlikely, particularly as you say you can compile earlier GROMACS versions with the same toolchain. The errors are caused by the compiler interpreting gmx_unused as a variable name, instead of a portable way to suppress compiler warnings about variables that are unused