Dear Users I figured out from the trailing mails as to how to use the "new installed version of CMAKE" for installing GROMACS
I used -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=......... . By default I think "icc" and "icpc" compilers were chosen. This step progressed smoothly. So , next I issued the command : "make". This step also completed without any error messages. However "make install" did not finish as expected. The installation process looked like a never ending process. Ultimately the following error message came up : terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc make: *** [install] Aborted I do not understand what to do next. I am thinking of using "gcc" and "g++" now. Kindly provide further suggestions. ------------------------------------------------------------------------------------------------------------------------------------ ---------- Forwarded message ---------- From: Mohd Farid Ismail <[email protected]> To: "[email protected]" <[email protected]>, " [email protected]" < [email protected]> Cc: Date: Sat, 08 Nov 2014 09:19:14 +0800 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster What he meant was to specify full path of your cmake, i.e. /work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY..... (and so on); instead of just typing cmake .. -DGMX_FFT_LIBRARY.... This is really a linux issue instead of gromacs. 08.11.2014, 06:00, "Agnivo Gosai" <[email protected]>: Dear Users 1 . I am not sure as to how to set the full path in the cmake command line. Do I need to use the export command to set the path ? An example will be of great help. I am also searching the web but can not find a satisfactory answer. As highlighted in my step 5 ( trailing mail ) , I think install_prefix will install the gromacs version in the specified directory or am I wrong ? 2. Yes , I understand it after reading the instructions. I think mdrun will pick up MPI threading automatically. I have also installed FFTW 3.0 in a local folder , how do I set its path in the cmake command line and I also have gcc in the root folder , along with icc. Pardon my ignorance as I think these are very basic questions related to the linux architecture. ---------- Forwarded message ---------- From: Justin Lemkul <[email protected]> To: [email protected] Cc: Date: Fri, 07 Nov 2014 16:26:56 -0500 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster On 11/7/14 4:20 PM, Agnivo Gosai wrote: Dear Users I checked and found that the CMAKE version installed in my university cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher. So I installed CMAKE 2.8.11 in my local work directory : /work/user/GROMACS/cmake-2.8/ bin/cmake Now I want to use Intel MKL , so after reading the GROMACS installation instruction I have decided to use the following workflow :- 1. tar xfz gromacs-4.6.7.tar.gz 2. cd gromacs-4.6.7 3. mkdir build 4. cd build 5. cmake .. -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON - DCMAKE_INSTALL_PREFIX=/work/user/GROMACS 6. make 7. make install Now when I check install location of CMAKE it points to the old version located in the Cluster root directory. Now , I want to use the new version which I believe to have installed correctly. So please help in solving this problem. Specify the full PATH of your cmake, otherwise the environment will just pick up the default cmake on the cluster. Also I would request the users to check my workflow of the installation process and provide suggestions. There is no point in compiling the whole suite of tools with MPI; nothing makes use of MPI except mdrun. So if you want to compile all the tools (preprocessing and analysis), don't set GMX_MPI. If you are using GMX_MPI, then set -DGMX_BUILD_MDRUN_ONLY=ON to get MPI-enabled mdrun. Strictly speaking, MPI is not required, but it depends on what you want to do whether or not you need it. -Justin ------------------------------------- Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
