[gmx-users] Reg Mpi run Error
Dear Jutin and Marks Thnak you for your previous reply Whrn i run the following job in cluster as follows [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v -deffnm CNTPEPRSOLIONSfull -cpt 2 I have eceived the error as follows Sisters Have Always Fascinated Me" (Speech) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 8 Halting parallel program mdrun_mpi on CPU 4 out of 8 gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_6]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 gcq#33: "Sisters Have Always Fascinated Me" (Speech) gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_3]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 [cli_2]: gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_5]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_4]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 65280 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES what is the meaning of above error How to solve it? Thanks in advance -- 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] Reg Mpi run Error
On 8/31/13 4:54 AM, vidhya sankar wrote: Dear Jutin and Marks Thnak you for your previous reply Whrn i run the following job in cluster as follows [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v -deffnm CNTPEPRSOLIONSfull -cpt 2 I have eceived the error as follows Sisters Have Always Fascinated Me" (Speech) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 8 Halting parallel program mdrun_mpi on CPU 4 out of 8 gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_6]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 gcq#33: "Sisters Have Always Fascinated Me" (Speech) gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_3]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 [cli_2]: gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_5]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 gcq#33: "Sisters Have Always Fascinated Me" (Speech) [cli_4]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 65280 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES what is the meaning of above error How to solve it? These are generic mpirun failure messages. The real error is further up in the screen output or in the .log file. -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] Reg mpirun error
Thank you justin for your reply The error I have pasted here (also pasted in previous mail) is total screen ouptut. No further output as you stated in previous mail( The real error is further up in the screen output or in the .log file.) > [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v -deffnm CNTPEPRSOLIONSfull -cpt 2 > > I have eceived the error as follows > Sisters Have Always Fascinated Me" (Speech) > Error on node 3, will try to stop all the nodes > Halting parallel program mdrun_mpi on CPU 3 out of 8 > Halting parallel program mdrun_mpi on CPU 4 out of 8 > gcq#33: "Sisters Have Always Fascinated Me" (Speech) > [cli_6]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 > gcq#33: "Sisters Have Always Fascinated Me" (Speech) > gcq#33: "Sisters Have Always Fascinated Me" (Speech) > [cli_3]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 > [cli_2]: > gcq#33: "Sisters Have Always Fascinated Me" (Speech) > [cli_5]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 > aborting job: > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 > gcq#33: "Sisters Have Always Fascinated Me" (Speech) > [cli_4]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 > > === > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 65280 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > you Mailed me this is generic mpirun error (These are generic mpirun failure messages) But No error message shown in .log file Could you please help to solve this error? With Regards S.Vidhyasankar -- 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] Reg mpirun error
Run it again, this time re-directing stderr and stdout to files so that you can read them later. (Google for how to do that with your shell.) Mark On Sat, Aug 31, 2013 at 1:47 PM, vidhya sankar wrote: > Thank you justin for your reply > > The error I have pasted here (also pasted in previous mail) > is total screen ouptut. No further output as you stated in previous mail( The > real error is further up in the > screen output or in the .log file.) > > > >> > [hinditron@compute002 gromacs-plumed-cpu-input]$ mpirun -np 8 > -machinefile ~/myhosts mdrun_mpi -s CNTPEPRSOLIONSfullcputest.tpr -v > -deffnm CNTPEPRSOLIONSfull -cpt 2 >> >> I have eceived the error as follows >> Sisters Have Always Fascinated Me" (Speech) >> Error on node 3, will try to stop all the nodes >> Halting parallel program mdrun_mpi on CPU 3 out of 8 >> Halting parallel program mdrun_mpi on CPU 4 out of 8 >> gcq#33: "Sisters Have Always Fascinated Me" (Speech) >> [cli_6]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 >> gcq#33: "Sisters Have Always Fascinated Me" (Speech) >> gcq#33: "Sisters Have Always Fascinated Me" (Speech) >> [cli_3]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 >> [cli_2]: >> gcq#33: "Sisters Have Always Fascinated Me" (Speech) >> [cli_5]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 >> aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 >> gcq#33: "Sisters Have Always Fascinated Me" (Speech) >> [cli_4]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 >> >> === >> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> = EXIT CODE: 65280 >> = CLEANING UP REMAINING PROCESSES >> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> > you Mailed me this is generic mpirun error (These are generic mpirun > failure messages) But No error message shown in .log file > > > Could you please help to solve this error? > > With Regards > S.Vidhyasankar > -- > 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
[gmx-users] grompy and how to call energy routine
Hi! I am currently using "mdrun -rerun" in order to get the energy of a system to be used in a Monte Carlo algortihm. A while ago, I was pointed to Grompy which should be capable of performing Monte Carlo using gromacs libraries (my description might not be very accurate here). I have downloaded grompy from git but I cannot find my way through (sorry, I'm rusty with python). Is there a way how I can directly call the gromacs energy routine from python and/or TCL? "mdrun -rerun" works but it creates overhead because the conformation has to be written to disk, then read by mdrun which writes an energy file that needs to be read by g_energy. I would like to have a library that can be called from my TCL/python script. I would appreciate any help on this. Thanks, Gianluca PS: According to the roadmap MC should be available in version 5.0 but until it's released I need to find an alternative :) - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] grompy and how to call energy routine
After reading a bit more in the grompy directory, I found that the file __init__.py loads the necessary libraries, e.g., mdrun.so. This is because gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I am using version 4.6.3 which uses "cmake" instead of "configure". Is there an equivalent flag for cmake that corresponds to "--enable-shared"? Thanks, Gianluca On Sat, 31 Aug 2013, Gianluca Interlandi wrote: Hi! I am currently using "mdrun -rerun" in order to get the energy of a system to be used in a Monte Carlo algortihm. A while ago, I was pointed to Grompy which should be capable of performing Monte Carlo using gromacs libraries (my description might not be very accurate here). I have downloaded grompy from git but I cannot find my way through (sorry, I'm rusty with python). Is there a way how I can directly call the gromacs energy routine from python and/or TCL? "mdrun -rerun" works but it creates overhead because the conformation has to be written to disk, then read by mdrun which writes an energy file that needs to be read by g_energy. I would like to have a library that can be called from my TCL/python script. I would appreciate any help on this. Thanks, Gianluca PS: According to the roadmap MC should be available in version 5.0 but until it's released I need to find an alternative :) - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] grompy and how to call energy routine
On 8/31/13 2:16 PM, Gianluca Interlandi wrote: After reading a bit more in the grompy directory, I found that the file __init__.py loads the necessary libraries, e.g., mdrun.so. This is because gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I am using version 4.6.3 which uses "cmake" instead of "configure". Is there an equivalent flag for cmake that corresponds to "--enable-shared"? -DBUILD_SHARED_LIBS=ON -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] question about g_hydorder
Dear all I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.Thanks in advance. -- 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] grompy and how to call energy routine
Thanks Justin. I have been wondering where I can find all options of cmake (./configure --help used to print all possible options, whereas cmake --help prints out just the usage of cmake itself). Gianluca On Sat, 31 Aug 2013, Justin Lemkul wrote: On 8/31/13 2:16 PM, Gianluca Interlandi wrote: After reading a bit more in the grompy directory, I found that the file __init__.py loads the necessary libraries, e.g., mdrun.so. This is because gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I am using version 4.6.3 which uses "cmake" instead of "configure". Is there an equivalent flag for cmake that corresponds to "--enable-shared"? -DBUILD_SHARED_LIBS=ON -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] grompy and how to call energy routine
On 8/31/13 2:32 PM, Gianluca Interlandi wrote: Thanks Justin. I have been wondering where I can find all options of cmake (./configure --help used to print all possible options, whereas cmake --help prints out just the usage of cmake itself). There's nothing like this that I'm aware of, but that's a problem on the CMake level, not the Gromacs level. There are lots of threads online asking the same thing. There are several methods for going through the CMake options, including interactively and/or via a GUI. See http://www.gromacs.org/Documentation/Installation_Instructions_4.5/Cmake. -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] grompy and how to call energy routine
I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun call libmd.so? Thanks, Gianluca On Sat, 31 Aug 2013, Justin Lemkul wrote: On 8/31/13 2:16 PM, Gianluca Interlandi wrote: After reading a bit more in the grompy directory, I found that the file __init__.py loads the necessary libraries, e.g., mdrun.so. This is because gromacs (they use version 4.0.7) was compiled with the flag --enable-shared. I am using version 4.6.3 which uses "cmake" instead of "configure". Is there an equivalent flag for cmake that corresponds to "--enable-shared"? -DBUILD_SHARED_LIBS=ON -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] grompy and how to call energy routine
On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun call libmd.so? I have never heard of anything called "libmdrun.so" and I do not see one in any of my current installations - 4.0.7, 4.5.5, or 4.6.3. The mdrun command should be linked against libmd.so; you can check with ldd. -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] grompy and how to call energy routine
On 8/31/13 3:11 PM, Justin Lemkul wrote: On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun call libmd.so? I have never heard of anything called "libmdrun.so" and I do not see one in any of my current installations - 4.0.7, 4.5.5, or 4.6.3. The mdrun command should be linked against libmd.so; you can check with ldd. A quick look through the GromPy documentation suggests that libmdrun.so is something that GromPy creates through one of its scripts. Having never used GromPy, that's the best I can offer. -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] grompy and how to call energy routine
Thanks for looking into that. I wonder whether routines of libmd.so can be called directly from a python script just like grompy calles routines from libmdrun.so I wonder if I can find more documentation about this topic. There is a python wrapper for gromacs functions here: http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/ and a thread in the developers discussion: http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html Gianluca On Sat, 31 Aug 2013, Justin Lemkul wrote: On 8/31/13 3:11 PM, Justin Lemkul wrote: On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun call libmd.so? I have never heard of anything called "libmdrun.so" and I do not see one in any of my current installations - 4.0.7, 4.5.5, or 4.6.3. The mdrun command should be linked against libmd.so; you can check with ldd. A quick look through the GromPy documentation suggests that libmdrun.so is something that GromPy creates through one of its scripts. Having never used GromPy, that's the best I can offer. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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] grompy and how to call energy routine
On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi wrote: > Thanks for looking into that. I wonder whether routines of libmd.so can be > called directly from a python script just like grompy calles routines from > libmdrun.so One could do so, but the GROMACS "libraries" are not built with this kind of usage in mind, and (for example) will issue a fatal error whenever that seems right. This will also kill the calling program, which is usually unacceptable. There's a current thread on gmx-users asking about library-type functionality, too. Better behaviour isn't likely to happen until someone steps up to make the code changes. So far it's not a priority for anyone who knows the code well enough to do it, and the learning curve too daunting for everyone else! :-) One doesn't have to hit disk with output files, either. Memory-mapped files and named pipes can be useful. Mark > I wonder if I can find more documentation about this topic. > > There is a python wrapper for gromacs functions here: > > http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/ > > and a thread in the developers discussion: > > http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html > > Gianluca > > > On Sat, 31 Aug 2013, Justin Lemkul wrote: > >> >> >> On 8/31/13 3:11 PM, Justin Lemkul wrote: >>> >>> >>> >>> On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun call libmd.so? >>> >>> I have never heard of anything called "libmdrun.so" and I do not see one >>> in any >>> of my current installations - 4.0.7, 4.5.5, or 4.6.3. The mdrun command >>> should >>> be linked against libmd.so; you can check with ldd. >>> >> >> A quick look through the GromPy documentation suggests that libmdrun.so is >> something that GromPy creates through one of its scripts. Having never used >> GromPy, that's the best I can offer. >> >> -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 >> > > - > Gianluca Interlandi, PhD gianl...@u.washington.edu > +1 (206) 685 4435 > http://artemide.bioeng.washington.edu/ > > Research Scientist at the Department of Bioengineering > at the University of Washington, Seattle WA U.S.A. > http://healthynaturalbaby.org > - > -- > 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] grompy and how to call energy routine
Dear Mark, Thank you very much for the enlightment. I will look into named pipes. This might be appropriate since I'm calling mdrun from a TCL script in VMD. Gianluca On Sun, 1 Sep 2013, Mark Abraham wrote: On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi wrote: Thanks for looking into that. I wonder whether routines of libmd.so can be called directly from a python script just like grompy calles routines from libmdrun.so One could do so, but the GROMACS "libraries" are not built with this kind of usage in mind, and (for example) will issue a fatal error whenever that seems right. This will also kill the calling program, which is usually unacceptable. There's a current thread on gmx-users asking about library-type functionality, too. Better behaviour isn't likely to happen until someone steps up to make the code changes. So far it's not a priority for anyone who knows the code well enough to do it, and the learning curve too daunting for everyone else! :-) One doesn't have to hit disk with output files, either. Memory-mapped files and named pipes can be useful. Mark I wonder if I can find more documentation about this topic. There is a python wrapper for gromacs functions here: http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/ and a thread in the developers discussion: http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003179.html Gianluca On Sat, 31 Aug 2013, Justin Lemkul wrote: On 8/31/13 3:11 PM, Justin Lemkul wrote: On 8/31/13 3:04 PM, Gianluca Interlandi wrote: I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries that I find are: libmd.so libgmxana.so libgmxpreprocess.so libgmx.so which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is no library called libmdrun.so like the one used in grompy. Could it be that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the command mdrun call libmd.so? I have never heard of anything called "libmdrun.so" and I do not see one in any of my current installations - 4.0.7, 4.5.5, or 4.6.3. The mdrun command should be linked against libmd.so; you can check with ldd. A quick look through the GromPy documentation suggests that libmdrun.so is something that GromPy creates through one of its scripts. Having never used GromPy, that's the best I can offer. -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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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 - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org - -- 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 ww
[gmx-users] Umbrella Sampling PMF
Hi, I ran US on an ion through a channel inserted in a bilayer. I used g_wham and got the profile output. In the visualized profile, I see a region that the plot shows a flat line and it seems the data is missed there. Would you please let me know what the reason of missing data is? Thanks for your suggestions in advance. Sincerely, Shima -- 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
