[gmx-users] gromacs build options

Hi, When trying to install gromacs-5.0, at this level: ''robert@robert-GL552JX:~/Downloads/gromacs-5.0/build$ cmake '/home/robert/Downloads/gromacs-5.0' -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON'' I get the following message after pressing enter and a few running:

Re: [gmx-users] gromacs build options

Thanks. Got it. Regards, Mahmood On Sun, Oct 9, 2016 at 2:36 PM, Mark Abraham wrote: > Hi, > > Great. But CMAKE_INSTALL_PREFIX and CMAKE_PREFIX_PATH are different things > that do different jobs (specify where to install vs where to search for > dependencies). > > Mark > > On Sun, Oct 9, 2016

Re: [gmx-users] gromacs build options

Hi, Great. But CMAKE_INSTALL_PREFIX and CMAKE_PREFIX_PATH are different things that do different jobs (specify where to install vs where to search for dependencies). Mark On Sun, Oct 9, 2016 at 12:20 PM Mahmood Naderan wrote: > Hi mark, > Thank you very much. In fact the following commands did

Re: [gmx-users] gromacs build options

Hi mark, Thank you very much. In fact the following commands did the job $ cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++ -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1 -DGMX_BUILD_OWN_FFTW=ON -DB

Re: [gmx-users] gromacs build options

Hi, On Sat, Oct 8, 2016 at 8:24 PM Mahmood Naderan wrote: > Sorry, but I got confused. I tried to follow the correct options to specify > > the location of libraries, bu failed... > Why did you change the setting that was working? FFTWF_LIBRARY wants a library, not a path in which to search for

Re: [gmx-users] gromacs build options

Sorry, but I got confused. I tried to follow the correct options to specify the location of libraries, bu failed... mahmood@cluster:build$ cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++ -DCMAKE_PREFIX_PAT

Re: [gmx-users] gromacs build options

Hi, On Sat, Oct 8, 2016 at 5:31 PM Mahmood Naderan wrote: > I got an error regarding fftw3. Maybe not related to GMX itself, but I > > appreciate any comment for that. > > > > > > root@cluster:build# Do not configure software as root, unless your preferred hobby is reinstalling operating syste

Re: [gmx-users] gromacs build options

I got an error regarding fftw3. Maybe not related to GMX itself, but I appreciate any comment for that. root@cluster:build# /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake .. -DCMAKE_C_COMPILER=/share/ap ps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi

Re: [gmx-users] gromacs build options

Yep. The build system notices that MPI is available, and you will see that it builds gmx_mpi, rather than gmx. gmx_mpi -version will confirm that the MPI library is not the built-in thread MPI. Mark On Sat, Oct 8, 2016 at 4:59 PM Mahmood Naderan wrote: > ​OK. I ran > > /share/apps/computer/cmak

Re: [gmx-users] gromacs build options

​OK. I ran /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++ -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1 -DBUILD_SHARED_LIBS=off please note that I

Re: [gmx-users] gromacs build options

Hi, This is the job of the wrapper compiler I've been telling you to use. Do any setup it requires, then cmake -DCMAKE_C_COMPILER=/path/to/mpicc -DCMAKE_CXX_COMPILER=/path/to/mpic++ It doesn't make sense to consider trying to use the same cmake option that you use to tell cmake where GROMACS wil

Re: [gmx-users] gromacs build options

​OMPI-2.0.1 is installed on the system. I want to tell gromacs that mpifort (or other wrappers) are in /share/apps/openmpi-2.0.1/bin and libraries are in /share/apps/opnempi-2.0.1/lib How can I tell that to cmake? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at ht

Re: [gmx-users] gromacs build options

Hi, If you're trying to install OpenMPI, please read its docs. That's a completely separate thing from installing GROMACS, and one you have to accomplish before e.g. trying to build GROMACS with support for that OpenMPI library, by using the newly installed wrapper compiler. Mark On Sat, Oct 8,

Re: [gmx-users] gromacs build options

​Excuse me, what I understood from the manual is that -DCMAKE_INSTALL_PREFIX is the same as --prefix in ./configure script. Do you mean that I can give multiple location with that option? One for the gromacs itself and the other for the MPI? I mean -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs-5.1 -D

Re: [gmx-users] gromacs build options

Hi, These are covered in the install guide... cmake -DCMAKE_INSTALL_PREFIX=/what/ever/you/want, and run whichever MPI wrapper compilers that you want (GROMACS doesn't care where they are located). Mark On Sat, Oct 8, 2016 at 12:14 PM Mahmood Naderan wrote: > Hi, > I am trying to install gromac

[gmx-users] gromacs build options

Hi, I am trying to install gromacs-5.1 from the source. What are the proper cmake options for the following things: 1- Installing to a custom location and not /usr/local 2- Using a customized installation of MPI and not /usr/local Regards, Mahmood -- Gromacs Users mailing list * Please search