Re: [gmx-users] Multi-level parallelization: MPI + OpenMP
I actually submitted using two MPI process per node but log files do not get updated, it's like the calculation gets stuck. Here is how I proceed: mpirun -np $NM -machinefile nodegpu mdrun_mpi -nb gpu -v -deffnm test184000atoms_verlet.tpr mdrun_mpi.log with the content of /nodegpu/: gpu04 gpu04 gpu11 gpu11 and with NM=`cat nodegpu | wc -l` /bjobs/ gives 3983hpceric RUN gpu mu0516*gpu11gromacsJul 19 12:12 16*gpu04 /mdrun_mpi.log/ contains the description of the options and /test184000atoms_verlet.tpr.log/ stops after PLEASE READ AND CITE THE FOLLOWING REFERENCE. The top of /test184000atoms_verlet.tpr.log/ is: Log file opened on Fri Jul 19 13:47:36 2013 Host: gpu11 pid: 124677 nodeid: 0 nnodes: 4 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Mon Jul 15 13:44:42 CST 2013 Built by: name@node [CMAKE] Build OS/arch: Linux 2.6.32-279.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicc GNU gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG C++ compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicxx GNU g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG CUDA compiler: /lustre/utility/cuda-5.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30;-use_fast_math;-Xcompiler;-fPIC ; -mavx;-Wextra;-Wno-missing-field-initializers;-Wno-sign-compare;-Wall;-Wno-unused;-Wunused-value;-fomit-frame-pointer;-funroll-all-loops;-O3;-DNDEBUG CUDA driver:5.0 CUDA runtime: 5.0 Does any have any idea about what's going wrong here? Thanks, Éric. On 07/19/2013 09:35 AM, Éric Germaneau wrote: Dear all, I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and making some test. Each node of our machine has 16 cores and 2 GPU. I'm trying to figure how to submit efficient multiple nodes LSF jobs using the maximum of resources. After reading the documentation http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores on Acceleration and parallelization I got confused and inquire some help. I'm just wondering whether someone with some experiences on this matter. I thank you in advance, Éric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Éric Germaneau http://hpc.sjtu.edu.cn/index.htm Shanghai Jiao Tong University Network Information Center room 205 Minhang Campus 800 Dongchuan Road Shanghai 200240 China View Éric Germaneau's profile on LinkedIn http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986 /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] QMMM number of thread
Dear Users; I would like to use Gromacs for QM/MM calculations. Up to now md calculations have been proceed without failure. Could you please shed on light on these issues related to the number of threads while using QM/MM interface with any kind of Quantum Chemistry software? 1-How many thread could be used during QM/MM calculation in Gromacs? 2-Does number of threads that are available for calculations depend on the software used for QM? 3-Can GROMACS handle QM/MM calculations by its own or need other simulation package (such as Gaussian, MOPAC, GAMESS) for QM/MM part? I am looking forward your kindly advices. regards, semran ipek küskü Istanbul Medeniyet University Engineering Physics Dept. ISTANBUL-TURKEI -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] QMMM number of thread
1.- You can only run the MD part in 1 thread, but you can perform the QM step with more procs. Note that, except for MOPAC, for which the library libmopac (see instructions in the website for how to get this) is directly used by the GROMACS code, the QM part consists in a external call to the QM package. In this call, you can use as many procs as you would use in any other call to the QM program. 2.- As said avobe, yes, the QM program manages its threads and memory independently, as it is a external call (except for MOPAC). 3.- Needs third party software (Gaussian, ORCA...) or the libmopac library provided at compilaton time. Javier El 19/07/13 08:49, SEMRAN İPEK escribió: Dear Users; I would like to use Gromacs for QM/MM calculations. Up to now md calculations have been proceed without failure. Could you please shed on light on these issues related to the number of threads while using QM/MM interface with any kind of Quantum Chemistry software? 1-How many thread could be used during QM/MM calculation in Gromacs? 2-Does number of threads that are available for calculations depend on the software used for QM? 3-Can GROMACS handle QM/MM calculations by its own or need other simulation package (such as Gaussian, MOPAC, GAMESS) for QM/MM part? I am looking forward your kindly advices. regards, semran ipek küskü Istanbul Medeniyet University Engineering Physics Dept. ISTANBUL-TURKEI -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] QMMM number of thread
Dear Javier; Thanks for comprehensive explanations for elusive part of QM/MM calculations. Best Regards, semran 2013/7/19 Javier Cerezo j...@um.es 1.- You can only run the MD part in 1 thread, but you can perform the QM step with more procs. Note that, except for MOPAC, for which the library libmopac (see instructions in the website for how to get this) is directly used by the GROMACS code, the QM part consists in a external call to the QM package. In this call, you can use as many procs as you would use in any other call to the QM program. 2.- As said avobe, yes, the QM program manages its threads and memory independently, as it is a external call (except for MOPAC). 3.- Needs third party software (Gaussian, ORCA...) or the libmopac library provided at compilaton time. Javier El 19/07/13 08:49, SEMRAN İPEK escribió: Dear Users; I would like to use Gromacs for QM/MM calculations. Up to now md calculations have been proceed without failure. Could you please shed on light on these issues related to the number of threads while using QM/MM interface with any kind of Quantum Chemistry software? 1-How many thread could be used during QM/MM calculation in Gromacs? 2-Does number of threads that are available for calculations depend on the software used for QM? 3-Can GROMACS handle QM/MM calculations by its own or need other simulation package (such as Gaussian, MOPAC, GAMESS) for QM/MM part? I am looking forward your kindly advices. regards, semran ipek küskü Istanbul Medeniyet University Engineering Physics Dept. ISTANBUL-TURKEI -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands: trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
On 7/19/13 4:17 AM, bipin singh wrote: According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands: trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. A 0.9-nm cubic box is likely too small to correctly accommodate even an amino acid, let alone an entire protein. -Justin On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Aw: Re: [gmx-users] How to calculate enthalpy
I thought about this reguaring solvation energy. If you use a good water model, and make a secoundary index for solvent (ie Solvent2 atoms x-xn), the normal Gromacs energy extraction would allow you to just extract all energy between protein and solvent2. I assume you could do some extreemly accurate solvation energy calculations this way, but the guassians for say 10-20 parallel runs of the same system would be much greater than say a protein-protein interaction. I am sure solvent models would have to be good as well, but may allow you to do what you wished, however I would make sure through others first, and I do not know what you wished to do completly. Stephan Watkins Gesendet:Montag, 15. Juli 2013 um 19:25 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Aw: Re: [gmx-users] How to calculate enthalpy Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)? And the energy of the internal structural hydrogen bonds that were disrupted? Assuming no acidic enviornment where electrons are involved...means of coarse... Gesendet:Montag, 15. Juli 2013 um 10:34 Uhr Von:pooja_gu...@nccs.res.in An:vvcha...@gmail.com, Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] How to calculate enthalpy Thanks Vitaly but how?? lets say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote: Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
Sorry for my silly mistake. I have a doubt regarding the expected difference in total No. of H-bonds calculated with whole a MD trajectory (protein+solvent box) and H-bonds calculated with concatenated frames (only protein) from a MD trajectory. I mean, will the number of H-bonds present at a particular time in a MD trajectory (protein+solvent), should be exactly same as number of H-bonds calculated using trajectory made of concatenated frames (only protein) from (if we look at number of H-bonds present at same point of time in both). Because I am not getting the exact match between the two, there is random difference of 1-3 H-bonds at some point of time. On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 4:17 AM, bipin singh wrote: According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands: trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. A 0.9-nm cubic box is likely too small to correctly accommodate even an amino acid, let alone an entire protein. -Justin On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GROMACS 4.6.3 Static Linking
Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/libxpmem.so.0 (0x7f50d52c9000) libdmapp.so.1 = /opt/cray/dmapp/default/lib64/libdmapp.so.1 (0x7f50d5092000) libugni.so.0 = /opt/cray/ugni/default/lib64/libugni.so.0 (0x7f50d4e72000) libpmi.so.0 = /opt/cray/pmi/default/lib64/libpmi.so.0 (0x7f50d4c51000) libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000) libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000) libudreg.so.0 = /opt/cray/udreg/default/lib64/libudreg.so.0 (0x7f50d4641000) libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/libgomp.so.1 (0x7f50d4432000) libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000) libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/libgcc_s.so.1 (0x7f50d3ebd000) /lib/ld64.so.1 = /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000) libquadmath.so.0 = /opt/gcc/4.7.2/snos/lib64/libquadmath.so.0 (0x7f50d3c87000) libcray_memcpy.so.0 = /opt/cray/lib64/libcray_memcpy.so.0 (0x7f50d3a84000) libopa.so.1 = /opt/cray/lib64/libopa.so.1 (0x7f50d3882000) librca.so.0 = /opt/cray/rca/default/lib64/librca.so.0 (0x7f50d367d000) libdl.so.2 = /lib64/libdl.so.2 (0x7f50d3479000) Any ideas? Andy = Dr Andrew R. Turner e: a.tur...@epcc.ed.ac.uk skype: aturner-epcc t: +44 (0)131 651 3578 p: EPCC, University of Edinburgh EH9 3JZ = -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.6.3 Static Linking
What does build_*/src/buildinfo.h have to say about the compiler flags that are getting used? Mark On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/libxpmem.so.0 (0x7f50d52c9000) libdmapp.so.1 = /opt/cray/dmapp/default/lib64/libdmapp.so.1 (0x7f50d5092000) libugni.so.0 = /opt/cray/ugni/default/lib64/libugni.so.0 (0x7f50d4e72000) libpmi.so.0 = /opt/cray/pmi/default/lib64/libpmi.so.0 (0x7f50d4c51000) libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000) libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000) libudreg.so.0 = /opt/cray/udreg/default/lib64/libudreg.so.0 (0x7f50d4641000) libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/libgomp.so.1 (0x7f50d4432000) libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000) libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/libgcc_s.so.1 (0x7f50d3ebd000) /lib/ld64.so.1 = /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000) libquadmath.so.0 = /opt/gcc/4.7.2/snos/lib64/libquadmath.so.0 (0x7f50d3c87000) libcray_memcpy.so.0 = /opt/cray/lib64/libcray_memcpy.so.0 (0x7f50d3a84000) libopa.so.1 = /opt/cray/lib64/libopa.so.1 (0x7f50d3882000) librca.so.0 = /opt/cray/rca/default/lib64/librca.so.0 (0x7f50d367d000) libdl.so.2 = /lib64/libdl.so.2 (0x7f50d3479000) Any ideas? Andy = Dr Andrew R. Turner e: a.tur...@epcc.ed.ac.uk skype: aturner-epcc t: +44 (0)131 651 3578 p: EPCC, University of Edinburgh EH9 3JZ = -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Multi-level parallelization: MPI + OpenMP
What's the simplest case you can make work? Mark On Fri, Jul 19, 2013 at 8:38 AM, Éric Germaneau german...@sjtu.edu.cn wrote: I actually submitted using two MPI process per node but log files do not get updated, it's like the calculation gets stuck. Here is how I proceed: mpirun -np $NM -machinefile nodegpu mdrun_mpi -nb gpu -v -deffnm test184000atoms_verlet.tpr mdrun_mpi.log with the content of /nodegpu/: gpu04 gpu04 gpu11 gpu11 and with NM=`cat nodegpu | wc -l` /bjobs/ gives 3983hpceric RUN gpu mu0516*gpu11gromacsJul 19 12:12 16*gpu04 /mdrun_mpi.log/ contains the description of the options and /test184000atoms_verlet.tpr.log/ stops after PLEASE READ AND CITE THE FOLLOWING REFERENCE. The top of /test184000atoms_verlet.tpr.log/ is: Log file opened on Fri Jul 19 13:47:36 2013 Host: gpu11 pid: 124677 nodeid: 0 nnodes: 4 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Mon Jul 15 13:44:42 CST 2013 Built by: name@node [CMAKE] Build OS/arch: Linux 2.6.32-279.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicc GNU gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG C++ compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicxx GNU g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG CUDA compiler: /lustre/utility/cuda-5.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30;-use_fast_math;-Xcompiler;-fPIC ; -mavx;-Wextra;-Wno-missing-field-initializers;-Wno-sign-compare;-Wall;-Wno-unused;-Wunused-value;-fomit-frame-pointer;-funroll-all-loops;-O3;-DNDEBUG CUDA driver:5.0 CUDA runtime: 5.0 Does any have any idea about what's going wrong here? Thanks, Éric. On 07/19/2013 09:35 AM, Éric Germaneau wrote: Dear all, I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and making some test. Each node of our machine has 16 cores and 2 GPU. I'm trying to figure how to submit efficient multiple nodes LSF jobs using the maximum of resources. After reading the documentation http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores on Acceleration and parallelization I got confused and inquire some help. I'm just wondering whether someone with some experiences on this matter. I thank you in advance, Éric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Éric Germaneau http://hpc.sjtu.edu.cn/index.htm Shanghai Jiao Tong University Network Information Center room 205 Minhang Campus 800 Dongchuan Road Shanghai 200240 China View Éric Germaneau's profile on LinkedIn http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986 /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the
Re: [gmx-users] GROMACS 4.6.3 Static Linking
Hi Mark, What does build_*/src/buildinfo.h have to say about the compiler flags that are getting used? /** C compiler flags used to build */ #define BUILD_CFLAGS-msse2-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -static -O3 -ftree-ve ctorize -ffast-math -funroll-loops -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG Cheers Andy = Dr Andrew R. Turner e: a.tur...@epcc.ed.ac.uk skype: aturner-epcc t: +44 (0)131 651 3578 p: EPCC, University of Edinburgh EH9 3JZ = -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond for trajectory without having box information
On 7/19/13 6:55 AM, bipin singh wrote: Sorry for my silly mistake. I have a doubt regarding the expected difference in total No. of H-bonds calculated with whole a MD trajectory (protein+solvent box) and H-bonds calculated with concatenated frames (only protein) from a MD trajectory. I mean, will the number of H-bonds present at a particular time in a MD trajectory (protein+solvent), should be exactly same as number of H-bonds calculated using trajectory made of concatenated frames (only protein) from (if we look at number of H-bonds present at same point of time in both). Because I am not getting the exact match between the two, there is random difference of 1-3 H-bonds at some point of time. I suspect that the issue stems from having to manually set the box. I don't understand why you would have to do this after running a simulation in explicit solvent. Did you just extract the protein coordinates from the explicit simulation? If so, I don't see how the box information would be omitted. You can get spurious H-bonds across PBC if you are manually setting a bad box size in a given frame or series of frames. Without the exact sequence of commands from what you have done, it's pure guesswork. -Justin On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 4:17 AM, bipin singh wrote: According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands: trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. A 0.9-nm cubic box is likely too small to correctly accommodate even an amino acid, let alone an entire protein. -Justin On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health
[gmx-users] .n2t file format
Dear gmx users I scrap lines from some files in oplsaa.ff folder as the following ffnonbonded file: [ atomtypes ] opls_157 CT6 12.01100 0.145 A3.5e-01 2.76144e-01 atomtypes.atp file: opls_157 12.01100 ; all-atom C: CH3 CH2, alcohols also, I looked at /gromacs /Documentation/file format/.n2t that written: To translate atom names into atom types, the x2top program uses library files called .n2t files as input. These files contain information about atom types, charges, and connectivity to neighbors. The format of such a file is exemplified by: *C* opls_157 -0.18 12.011 4 H 0.108 H 0.108 H 0.108 C 0.150 The above line interprets an atom named C to be the carbon atom in CH3, CH2, or alcohols (atom type opls_157). My question is that carbon atomname with opls_157 atomtype is *C* or CT? In other word the first column in .n2t is atomneme (CT as mentioned in ffnonbonded file ) or element name (C as mentioned in file format.n2t )? Also, are 6, 8 10 columns atomname or element name? Any help is much appreciated Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .n2t file format
On 7/19/13 8:20 AM, afsaneh maleki wrote: Dear gmx users I scrap lines from some files in oplsaa.ff folder as the following ffnonbonded file: [ atomtypes ] opls_157 CT6 12.01100 0.145 A3.5e-01 2.76144e-01 atomtypes.atp file: opls_157 12.01100 ; all-atom C: CH3 CH2, alcohols also, I looked at /gromacs /Documentation/file format/.n2t that written: To translate atom names into atom types, the x2top program uses library files called .n2t files as input. These files contain information about atom types, charges, and connectivity to neighbors. The format of such a file is exemplified by: *C* opls_157 -0.18 12.011 4 H 0.108 H 0.108 H 0.108 C 0.150 The above line interprets an atom named C to be the carbon atom in CH3, CH2, or alcohols (atom type opls_157). My question is that carbon atomname with opls_157 atomtype is *C* or CT? The type is opls_157 for the purposes of ffnonbonded.itp, which is translated to the CT in ffbonded.itp. In other word the first column in .n2t is atomneme (CT as mentioned in ffnonbonded file ) or element name (C as mentioned in file format.n2t )? In Gromacs nomenclature, atom names are whatever is read from the input coordinate file (no differentiation between atom name and element name) and atom types are force field-specific. Also, are 6, 8 10 columns atomname or element name? Both, given Gromacs' interpretation of atom names. g_x2top will look for matches based on whatever element it finds, so in the case of column 6, any of these will match: H, HA, H1, H2, etc. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generate topology
Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Multi-level parallelization: MPI + OpenMP
Depending on the level of parallelization (number of nodes and number of particles/core) you may want to try: - 2 ranks/node: 8 cores + 1 GPU, no separate PME (default): mpirun -np 2*Nnodes mdrun_mpi [-gpu_id 01 -npme 0] - 4 ranks per node: 4 cores + 1 GPU (shared between two ranks), no separate PME mpirun -np 4*Nnodes mdrun_mpi -gpu_id 0011 [-npme 0] - 4 ranks per node, 2 PP/2PME: 4 cores + 1 GPU (not shared), separate PME mpirun -np 4*Nnodes mdrun_mpi [-gpu_id 01] -npme 2*Nnodes - at high parallelization you may want to try (especially with homogeneous systems) 8 ranks per node Cheers, -- Szilárd On Fri, Jul 19, 2013 at 4:35 AM, Éric Germaneau german...@sjtu.edu.cn wrote: Dear all, I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and making some test. Each node of our machine has 16 cores and 2 GPU. I'm trying to figure how to submit efficient multiple nodes LSF jobs using the maximum of resources. After reading the documentation http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores on Acceleration and parallelization I got confused and inquire some help. I'm just wondering whether someone with some experiences on this matter. I thank you in advance, Éric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Éric Germaneau http://hpc.sjtu.edu.cn/index.htm Shanghai Jiao Tong University Network Information Center room 205 Minhang Campus 800 Dongchuan Road Shanghai 200240 China View Éric Germaneau's profile on LinkedIn http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986 /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generate topology
On 7/19/13 8:53 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generate topology
Dear Justin thanks for your reply, I did it. when I put the .n2t in my working directory,I have gotten this error. thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generate topology
On 7/19/13 9:10 AM, afsaneh maleki wrote: Dear Justin thanks for your reply, I did it. when I put the .n2t in my working directory,I have gotten this error. What error? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generate topology -2
Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I edited atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms for more information and tips for troubleshooting, ……….. I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as the above mentioned in my working directory. How to solve my problem? Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? Thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generate topology -2
On 7/19/13 9:32 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I edited atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms for more information and tips for troubleshooting, ……….. I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as the above mentioned in my working directory. How to solve my problem? Why do gromacs open / usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? Let's not go backwards. I responded to this post already and you gave a cryptic reply about some new error. Please respond to the other post. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generate topology
Dear Justin I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as mentioned in before post in my working directory. I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……….. I seem can't read atomname2type.n2t file from my working directory. Thanks very much. Afsaneh On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 8:53 AM, afsaneh maleki wrote: Dear Justin I want a topology for an arbitrary molecule (44 atom) and I use x2top program that .n2t file is it’s input. The .pdb file is as the following: ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00 ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00 ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.00 ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.00 ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.00 ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.00 ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.00 …… I copied oplsaa.ff folder in my working directory atomname2type.n2t file is as the following: O opls_267 -0.495284 15.9994 1 C 0.1214 C opls_4700.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 H opls_2700.4173341.0079 1 O 0.0974 C opls_1450.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 H opls_1460.1108421.0079 1 C 0.1087 …… I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa But I get: opening force field file /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 *Fatal error:* Could only find a forcefield type for 32 out of 44 atoms. How to solve my problem. Why do gromacs open / usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t? I copyied oplsaa.ff folder in my working directory. Also I edited .n2t file in my folder. Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] Generate topology
On 7/19/13 10:06 AM, afsaneh maleki wrote: Dear Justin I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as mentioned in before post in my working directory. I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ……….. I seem can't read atomname2type.n2t file from my working directory. Use -ff select to choose the force field that resides in the working directory. Specifying -ff oplsaa tells g_x2top to use the oplsaa.ff directory in $GMXLIB. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problems with REMD in Gromacs 4.6.3
Hi! On 2013-07-17 21:08, Mark Abraham wrote: You tried ppn3 (with and without --loadbalance)? I was testing on 8-replicas simulation. 1) Without --loadbalance and -np 8. Excerpts from the script: #PBS -l nodes=8:ppn=3 setenv OMP_NUM_THREADS 4 mpiexec mdrun_mpi -v -cpt 20 -multi 8 -ntomp 4 -replex 2500 -cpi -pin on Excerpts from logs: Using 3 MPI processes Using 4 OpenMP threads per MPI process (...) Overriding thread affinity set outside mdrun_mpi Pinning threads with an auto-selected logical core stride of 1 WARNING: In MPI process #0: Affinity setting for 1/4 threads failed. This can cause performance degradation! If you think your setting are correct, contact the GROMACS developers. WARNING: In MPI process #2: Affinity setting for 4/4 threads failed. Load: The job was allocated 24 cores (3 cores on 8 different nodes). Each OpenMP thread uses ~1/3 of a CPU core on average. Conclusions: MPI runs as many processes as cores requested (nnodes*ppn=24), it ignores OMP_NUM_THREADS env == this is wrong and is not Gromacs issue. Each MPI process forks to 4 threads as requested. The 24-core limit granted by Torque is not violated. 2) The same script, but with -np 8, to limit the number of MPI processes to the number of replicas Logs: Using 1 MPI process Using 4 OpenMP threads (...) Replicas 0,3 and 6: WARNING: Affinity setting for 1/4 threads failed. Replicas 1,2,4,5,7: WARNING: Affinity setting for 4/4 threads failed. Load: The job was allocated 24 cores on 8 nodes. Only on first 3 nodes mpiexec was run. Each OpenMP thread uses ~20% of a CPU core. 3) -np 8 --loadbalance Excerpts from logs: Using 1 MPI process Using 4 OpenMP threads (...) Each replica says: WARNING: Affinity setting for 3/4 threads failed. Load: MPI processes spread evenly on all 8 nodes. Each OpenMP thread uses ~50% of a CPU core. 4) -np 8 --loadbalance, #PBS -l nodes=8:ppn=4 == this worked ~OK with gromacs 4.6.2 Logs: WARNING: Affinity setting for 2/4 threads failed. Load: 32 cores allocated on 8 nodes. MPI processes spread evenly, each OpenMP thread uses ~70% of a CPU core. With 144 replicas the simulation did not produce any results, just got stuck. Some thoughts: the main problem is most probably in the way MPI interprets the information from torque, it is not Gromacs related. MPI ignores OMP_NUM_THREADS. The environment is just broken. Since gromacs-4.6.2 behaved better than 4.6.3 there, I am coming back to it. Best, G Mark On Wed, Jul 17, 2013 at 6:30 PM, gigo g...@ibb.waw.pl wrote: On 2013-07-13 11:10, Mark Abraham wrote: On Sat, Jul 13, 2013 at 1:24 AM, gigo g...@ibb.waw.pl wrote: On 2013-07-12 20:00, Mark Abraham wrote: On Fri, Jul 12, 2013 at 4:27 PM, gigo g...@ibb.waw.pl wrote: Hi! On 2013-07-12 11:15, Mark Abraham wrote: What does --loadbalance do? It balances the total number of processes across all allocated nodes. OK, but using it means you are hostage to its assumptions about balance. Thats true, but as long as I do not try to use more resources that the torque gives me, everything is OK. The question is, what is a proper way of running multiple simulations in parallel with MPI that are further parallelized with OpenMP, when pinning fails? I could not find any other. I think pinning fails because you are double-crossing yourself. You do not want 12 MPI processes per node, and that is likely what ppn is setting. AFAIK your setup should work, but I haven't tested it. The thing is that mpiexec does not know that I want each replica to fork to 4 OpenMP threads. Thus, without this option and without affinities (in a sec about it) mpiexec starts too many replicas on some nodes - gromacs complains about the overload then - while some cores on other nodes are not used. It is possible to run my simulation like that: mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi (without --loadbalance for mpiexec and without -ntomp for mdrun) Then each replica runs on 4 MPI processes (I allocate 4 times more cores then replicas and mdrun sees it). The problem is that it is much slower than using OpenMP for each replica. I did not find any other way than --loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to use MPI and OpenMP at the same time on the torque-controlled cluster. That seems highly surprising. I have not yet encountered a job scheduler that was completely lacking a do what I tell you layout scheme. More importantly, why are you using #PBS -l nodes=48:ppn=12? I thing that torque is very similar to all PBS-like resource managers in this regard. It actually does what I tell it to do. There are 12-core nodes, I ask for 48 of them - I get them (simple #PBS -l ncpus=576 does not work), end of story. Now, the program that I run is responsible for populating resources that I got. No, that's not the end of the story. The scheduler and the MPI system typically cooperate to populate
