>>>I am thinking of using "gcc" and "g++" now. Kindly provide further suggestions.
http://hpc.ucla.edu/hoffman2/software/compilers http://lmgtfy.com/?q=difference+between+gcc+and+g%2B%2B http://lmgtfy.com/?q=gcc+compiler+installation+linux <https://mail.google.com/mail/u/0/?ui=2&ik=4d6c0a5051&view=att&th=149643f024d7d537&attid=0.1&disp=safe&realattid=f_i1wzdfrg0&zw> On Sun, Nov 9, 2014 at 9:42 AM, Agnivo Gosai <[email protected]> wrote: > 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]. > -- 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].
