Re: [gmx-users] Regarding gromacs installation
Dear Sathya, You might have done this but anyway I do the installation using following commands, export CMAKE_PREFIX_INSTALL=/share/apps/fftw/3.3.4-gcc-4.8.2 cmake .. -DGMX_OPENMP=ON -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/5 make -j16 make install I make sure that the install path is in env. var. $PATH export PATH=$PATH:/share/apps/gromacs/5 Regards, Dinesh Mali On Wed, Sep 3, 2014 at 10:02 PM, Sathya bti027.2...@gmail.com wrote: Hi I have installed cmake version 2.8.12.2 and gromacs 4.6.3 in centOS. During installation there was no error. But i didnt get information like Gromacs has been successfully installed. When i use pdb2gmx or mdrun commands it is showing command not found. I dont know what is the problem and how should i rectify it. Please help me to solve this. -- With regards, Sathya.B -- 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 gmx-users-requ...@gromacs.org. -- Dinesh Mali Systems Engineer Locuz Enterprise Solutions Ltd. Bangalore -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Suggestions for Gromacs Perfomance
Dear gmx users, I have been performing some benchmarks as given taken from following URL, http://www.gromacs.org/GPU_acceleration The expected performance values is taken from the graph s . This cluster has a two nodes, of which one has two Nvidia K20 gpus. I have follo wed the performance checklist given in following URL, http://www. gromacs.org/Documentation/Performance_checklist http://www.gromacs.org/Documentation/Performance_checklist I am using fftw-3.3.4 with sse2 SIMD instructions and using cuda-5.5. The results are as follows: Gromacs Version 4.6.5 GCC Version 4.4.6 System CPU/GPU used performance(ns/day) expected(ns/day) RNASE 2 CPU (Cores 16, nopm 1) 63.815 80 RNASE 1CPU(8cores)+1GPU (-gpu_id ) 50.647 95 ADH 4 CPU on 2 on each node (32 Cores) 15.115 15 Gromacs Version 5.0.0 GCC Version 4.7.2 System CPU/GPU used performance(ns/day) expected(ns/day) RNASE 2 CPU (Cores 16, nopm 1)66.698 80 RNASE 1CPU(8cores)+1GPU (-np 8 -gpu_id ) 47.763 95 ADH 4 CPU on 2 on each node (32 Cores) 14.142 15 Kindly provide inputs to improve the performance with gpus . Also, if possible please suggest simulation with reported performance simulation for performing benchmarks for both CPU GPU. Regards, Dinesh Mali -- 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 gmx-users-requ...@gromacs.org.
