Re: [gmx-users] install and mdrun problems
Hello Sir, I hope you are good and doing well. With such settings, I would do the following steps 1. Make up to date the system BIOS. 2. Double Check the appropriate installation of GROMACS dependencies *viz.*, MPI thread, Open MP threads, *etc. * 3. Re-install gmx 4. Re-install Ubuntu and gmx 5. Sudo apt-get update 6. gmx info Just for example, please find a link for MD-Certified systems/engines up to 1000 ns/ day <https://www.exxactcorp.com/Molecular-Dynamics-Solutions> for personal/multi-user environments. I hope it helps. Sincerely, Kunal [kunal_lif...@mail.vidyasagar.ac.in] On Mon, 2 Mar 2020 at 22:07, Bogdanov, Vladimir wrote: > Hi Kunal, > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. > > It looks like the reason of my PC shut down is lying in the Bios settings, > but I don't know the version of BIOS, I can look it later, if you need. > -- > *From:* gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Kunal > Dutta > *Sent:* Monday, March 2, 2020 8:56 AM > *To:* gmx-us...@gromacs.org > *Cc:* gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se> > *Subject:* Re: [gmx-users] install and mdrun problems > > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before > > posting! > > > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > *--Every life is precious* > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or send a mail to gmx-users-requ...@gromacs.org. > -- *--Every life is precious* -- 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.
Re: [gmx-users] install and mdrun problems
Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > 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. > -- *--Every life is precious* -- 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.
Re: [gmx-users] How good to use triclinic box for gormacs simulations?
Hi, Please check the link. http://manual.gromacs.org/programs/gmx-editconf.html Best, Kunal On Tue, Oct 31, 2017 at 3:22 AM, vijayakumar gosu <vijayakumarg...@gmail.com > wrote: > Hello all, > > > I have performed simulations for Protein RNA complex around 1500 residues. > I have used triclinic box with 1.4 nm distance from the edge of the box to > protein as triclinic box takes less number of water molecules (~10) > compared to other boxes . The simulation results looks fine and i am able > to answer the biological question. however i have not seen many > publications using triclinic box. Hence i am bit skeptical and like to > know there is any criteria to choose the simulation box. > > > Thanks > -- > 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. > -- - Regards. Kunal Dutta Senior Research Scholar Microbiology and Immunology Laboratory Department of Human Physiology with Community Health Vidyasagar University, Medinipur-721102 West Bengal, India. Cell: 9126181933 ORCID ID: -0002-0818-8787 RG: https://www.researchgate.net/profile/Kunal_Dutta2 GS: https://scholar.google.co.in/citations?user=ULby284J=en -- *CONFIDENTIALITY NOTICE* This communication (including any attachment/s) is intended only for the use of the addressee(s) and contains information that is PRIVILEGED AND CONFIDENTIAL. Unauthorized reading, dissemination, distribution, or copying of this communication is prohibited. *DISCLAIMER* Any views or opinions presented in this email are solely those of the author and do not necessarily represent those the University. WARNING:- This communication, including any attachments, may not be free of viruses, interceptions or interference, and may not be compatible with your systems. You should carry out your own virus checks before opening any attachment to this e-mail. The sender of this e-mail and Vidyasagar University shall not be liable for any damage that you may sustain as a result of viruses, incompleteness of this message, a delay in receipt of this message or computer problems experienced. -- 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] Gromacs error
Hi, I have the following problems kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message): The GROMACS build will download FFTW 3.3.3 as requested, but it will not know the file it receives is correct. If you now use make GROMACS will build and link to FFTW anyway, but there is a possible security risk if you execute a GROMACS tool that calls this library. Instead, you can use make fftwBuild to do just the download and build of FFTW, and then run md5sum src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.3.tar.gz to see if it matches 0a05ca9c7b3bfddc8278e7c40791a1c2. If so, everything is OK and you should use make to proceed with the rest of the GROMACS build. Alternatively, you could stop using GMX_BUILD_OWN_FFTW, and instead follow the GROMACS installation instructions to build FFTW yourself. -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring done -- Generating done -- Build files have been written to: /home/kunal/Downloads/gromacs-5.0/build kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ make [ 1%] Built target fftwBuild [ 1%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o /usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const void*, size_t)’: /usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope return (char *) memcpy (__dest, __src, __n) + __n; ^ CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:264 (message): Error generating file /home/kunal/Downloads/gromacs-5.0/build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make:383: recipe for target 'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o' failed make[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] Error 1 CMakeFiles/Makefile2:1609: recipe for target 'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all' failed make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2 -- - Regards. Kunal Dutta Senior Research Scholar Microbiology and Immunology Laboratory Department of Human Physiology with Community Health Vidyasagar University, Medinipur-721102 West Bengal, India. Cell: 9126181933 ORCID ID: -0002-0818-8787 RG: https://www.researchgate.net/profile/Kunal_Dutta2 GS: https://scholar.google.co.in/citations?user=ULby284J=en -- *CONFIDENTIALITY NOTICE* This communication (including any attachment/s) is intended only for the use of the addressee(s) and contains information that is PRIVILEGED AND CONFIDENTIAL. Unauthorized reading, dissemination, distribution, or copying of this communication is prohibited. *DISCLAIMER* Any views or opinions presented in this email are solely those of the author and do not necessarily represent those the University. WARNING:- This communication, including any attachments, may not be free of viruses, interceptions or interference, and may not be compatible with your systems. You should carry out your own virus checks before opening any attachment to this e-mail. The sender of this e-mail and Vidyasagar University shall not be liable for any damage that you may sustain as a result of viruses, incompleteness of this message, a delay in receipt of this message or computer problems experienced. -- 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.
