Re: [gmx-users] Replica Exchange MD on more than 64 processors
On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos - REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the system at respective temperatures (total of 35 equilibration simulations). After this I generated chk_0.tpr, chk_1.tpr, ..., chk_34.tpr files from the equilibrated structures. Now when I submit final job for REMD with following command-line, it gives some error: command line: mpiexec -np 70 mdrun -multi 35 -replex 1000 -s chk_.tpr -v error msg: --- Program mdrun_mpi, VERSION 4.0.7 Source code file: ../../../SRC/src/gmxlib/smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0x9a400030 (called from file ../../../SRC/src/mdlib/ns.c, line 503) --- Thanx for Using GROMACS - Have a Nice Day : Cannot allocate memory Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 19 out of 70 *** The individual node on the cluster has 8GB of physical memory and 16GB of swap memory. Moreover, when logged onto the individual nodes, it shows more than 1GB of free memory, so there should be no problem with cluster memory. Also, the equilibration jobs for the same system are run on the same cluster without any problem. What I have observed by submitting different test jobs with varying number of processors (and no. of replicas, wherever necessary), that any job with total number of processors = 64, runs faithfully without any problem. As soon as total number of processors are more than 64, it gives the above error. I have tested this with 65 processors/65 replicas also. This sounds like you might be running on fewer physical CPUs than you have available. If so, running multiple MPI processes per physical CPU can lead to memory shortage conditions. I don't understand what you mean. Do you mean, there might be more than 8 processes running per node (each node has 8 processors)? But that also does not seem to be the case, as SGE (sun grid engine) output shows only eight processes per node. I don't know what you mean by swap memory. Sorry, I meant cache memory.. bharat Mark System: Protein + water + Na ions (total 46878 atoms) Gromacs version: tested with both v4.0.5 and v4.0.7 compiled with: --enable-float --with-fft=fftw3 --enable-mpi compiler: gcc_3.4.6 -O3 machine details: uname -mpio: x86_64 x86_64 x86_64 GNU/Linux I tried searching the mailing-list without any luck. I am not sure, if i am doing anything wrong in giving commands. Please correct me if it is wrong. Kindly let me know the solution. bharat -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD on more than 64 processors
bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos - REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the system at respective temperatures (total of 35 equilibration simulations). After this I generated chk_0.tpr, chk_1.tpr, ..., chk_34.tpr files from the equilibrated structures. Now when I submit final job for REMD with following command-line, it gives some error: command line: mpiexec -np 70 mdrun -multi 35 -replex 1000 -s chk_.tpr -v error msg: --- Program mdrun_mpi, VERSION 4.0.7 Source code file: ../../../SRC/src/gmxlib/smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0x9a400030 (called from file ../../../SRC/src/mdlib/ns.c, line 503) --- Thanx for Using GROMACS - Have a Nice Day : Cannot allocate memory Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 19 out of 70 *** The individual node on the cluster has 8GB of physical memory and 16GB of swap memory. Moreover, when logged onto the individual nodes, it shows more than 1GB of free memory, so there should be no problem with cluster memory. Also, the equilibration jobs for the same system are run on the same cluster without any problem. What I have observed by submitting different test jobs with varying number of processors (and no. of replicas, wherever necessary), that any job with total number of processors = 64, runs faithfully without any problem. As soon as total number of processors are more than 64, it gives the above error. I have tested this with 65 processors/65 replicas also. This sounds like you might be running on fewer physical CPUs than you have available. If so, running multiple MPI processes per physical CPU can lead to memory shortage conditions. I don't understand what you mean. Do you mean, there might be more than 8 processes running per node (each node has 8 processors)? But that also does not seem to be the case, as SGE (sun grid engine) output shows only eight processes per node. 65 processes can't have 8 processes per node. Mark I don't know what you mean by swap memory. Sorry, I meant cache memory.. bharat Mark System: Protein + water + Na ions (total 46878 atoms) Gromacs version: tested with both v4.0.5 and v4.0.7 compiled with: --enable-float --with-fft=fftw3 --enable-mpi compiler: gcc_3.4.6 -O3 machine details: uname -mpio: x86_64 x86_64 x86_64 GNU/Linux I tried searching the mailing-list without any luck. I am not sure, if i am doing anything wrong in giving commands. Please correct me if it is wrong. Kindly let me know the solution. bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD on more than 64 processors
On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos - REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the system at respective temperatures (total of 35 equilibration simulations). After this I generated chk_0.tpr, chk_1.tpr, ..., chk_34.tpr files from the equilibrated structures. Now when I submit final job for REMD with following command-line, it gives some error: command line: mpiexec -np 70 mdrun -multi 35 -replex 1000 -s chk_.tpr -v error msg: --- Program mdrun_mpi, VERSION 4.0.7 Source code file: ../../../SRC/src/gmxlib/smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0x9a400030 (called from file ../../../SRC/src/mdlib/ns.c, line 503) --- Thanx for Using GROMACS - Have a Nice Day : Cannot allocate memory Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 19 out of 70 *** The individual node on the cluster has 8GB of physical memory and 16GB of swap memory. Moreover, when logged onto the individual nodes, it shows more than 1GB of free memory, so there should be no problem with cluster memory. Also, the equilibration jobs for the same system are run on the same cluster without any problem. What I have observed by submitting different test jobs with varying number of processors (and no. of replicas, wherever necessary), that any job with total number of processors = 64, runs faithfully without any problem. As soon as total number of processors are more than 64, it gives the above error. I have tested this with 65 processors/65 replicas also. This sounds like you might be running on fewer physical CPUs than you have available. If so, running multiple MPI processes per physical CPU can lead to memory shortage conditions. I don't understand what you mean. Do you mean, there might be more than 8 processes running per node (each node has 8 processors)? But that also does not seem to be the case, as SGE (sun grid engine) output shows only eight processes per node. 65 processes can't have 8 processes per node. why can't it have? as i said, there are 8 processors per node. what i have not mentioned is that how many nodes it is using. The jobs got distributed over 9 nodes. 8 of which corresponds to 64 processors + 1 processor from 9th node. As far I can tell you, job distribution seems okay to me. It is 1 job per processor. bharat Mark I don't know what you mean by swap memory. Sorry, I meant cache memory.. bharat Mark System: Protein + water + Na ions (total 46878 atoms) Gromacs version: tested with both v4.0.5 and v4.0.7 compiled with: --enable-float --with-fft=fftw3 --enable-mpi compiler: gcc_3.4.6 -O3 machine details: uname -mpio: x86_64 x86_64 x86_64 GNU/Linux I tried searching the mailing-list without any luck. I am not sure, if i am doing anything wrong in giving commands. Please correct me if it is wrong. Kindly let me know the solution. bharat -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] tpr older version message
If I preped the tpr using amber forcefields, could that be the reason? The mdrun I am using does not have any force field libraries in its directory. On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- I'd say it's evident that if the file is not corrupted (use gmxcheck), the GROMACS installations weren't the same (unmodified) version. Reproduce the conditions and run grompp -h to inspect the version. Perhaps you are having a problem with a shared-library mismatch. If you have such an old version of GROMACS around, either uninstall it and retire the sysadmin, or send the computer to a museum :-) Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.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/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/mailing_lists/users.php
[gmx-users] fix a group in truncated octahedron
Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid body, so that no matter how large force between them shoud not blow up the rigid body. How can I do this? Thanks in advance. -- wende -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] fix a group in truncated octahedron
Hi Wende, please do not double post. If you are unsure if your post got through, you can easily see the list at http://lists.gromacs.org/pipermail/gmx-users/2009-December/date.html. You did not put units beside 40, so I suppose that you mean 40 A, whereas gromacs uses nm. 1. Make a box with one sodium ion and then editconf -c -d 4 -bt dodecahedron. This will give you your box, then you can put your lattice inside it. With properly selected atom in an index file, you could easily do this in one step based on the commands above (plus the index group with a single central atom). 2. This is clearly laid out in the manual under energygrp_excl. You should familiarize yourself with the online .mdp file options at http://manual.gromacs.org/current/online/mdp_opt.html which will help you find such things. Chris. -- original message -- Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid body, so that no matter how large force between them shoud not blow up the rigid body. How can I do this? Thanks in advance. -- wende -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Decoupling of Coul. and LJ separately in free energy calculation
Dear GMX users, it is recommended the use of two-step procedure for decoupling the solute from the solvent in hydration free energy calculation: first decreasing the charges in the solute, without soft core, and after that, the same procedure is used for the LJ interactions. In version Gromacs 4, how can I do this by using the options couple-moltype(lambda0,lambda1,intramol)? I'm unsure about the use of these options for this purpose. Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD on more than 64 processors
bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos - REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the system at respective temperatures (total of 35 equilibration simulations). After this I generated chk_0.tpr, chk_1.tpr, ..., chk_34.tpr files from the equilibrated structures. Now when I submit final job for REMD with following command-line, itgives some error: command line: mpiexec -np 70 mdrun -multi 35 -replex 1000 -s chk_.tpr-v error msg: --- Program mdrun_mpi, VERSION 4.0.7 Source code file: ../../../SRC/src/gmxlib/smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0x9a400030 (called from file ../../../SRC/src/mdlib/ns.c, line 503) --- Thanx for Using GROMACS - Have a Nice Day : Cannot allocate memory Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 19 out of 70 *** The individual node on the cluster has 8GB of physical memory and 16GBof swap memory. Moreover, when logged onto the individual nodes, it shows more than 1GB of free memory, so there should be no problem withcluster memory. Also, the equilibration jobs for the same system are run on the same cluster without any problem. What I have observed by submitting different test jobs with varyingnumber of processors (and no. of replicas, wherever necessary), that any jobwith total number of processors = 64, runs faithfully without any problem.As soon as total number of processors are more than 64, it gives the above error. I have tested this with 65 processors/65 replicas also. This sounds like you might be running on fewer physical CPUs than you have available. If so, running multiple MPI processes per physical CPU can lead to memory shortage conditions. I don't understand what you mean. Do you mean, there might be more than 8 processes running per node (each node has 8 processors)? But that also does not seem to be the case, as SGE (sun grid engine) output shows only eight processes per node. 65 processes can't have 8 processes per node. why can't it have? as i said, there are 8 processors per node. what i have not mentioned is that how many nodes it is using. The jobs got distributed over 9 nodes. 8 of which corresponds to 64 processors + 1 processor from 9th node. OK, that's a full description. Your symptoms are indicative of someone making an error somewhere. Since GROMACS works over more than 64 processors elsewhere, the presumption is that you are doing something wrong or the machine is not set up in the way you think it is or should be. To get the most effective help, you need to be sure you're providing full information - else we can't tell which error you're making or (potentially) eliminate you as a source of error. As far I can tell you, job distribution seems okay to me. It is 1 job per processor. Does non-REMD GROMACS run on more than 64 processors? Does your cluster support using more than 8 nodes in a run? Can you run an MPI Hello world application that prints the processor and node ID across more than 64 processors? Mark bharat Mark I don't know what you mean by swap memory. Sorry, I meant cache memory.. bharat Mark System: Protein + water + Na ions (total 46878 atoms) Gromacs version: tested with both v4.0.5 and v4.0.7 compiled with: --enable-float --with-fft=fftw3 --enable-mpi compiler: gcc_3.4.6 -O3 machine details: uname -mpio: x86_64 x86_64 x86_64 GNU/Linux I tried searching the mailing-list without any luck. I am not sure, ifi am doing anything wrong in giving commands. Please correct me if it is wrong. Kindly let me know the solution. bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] tpr older version message
Jack Shultz wrote: If I preped the tpr using amber forcefields, could that be the reason? No. The mdrun I am using does not have any force field libraries in its directory. That's irrelevant. Only non-mdrun tools care about the contents of $GMXLIB or local force field files. The point of GROMPP is that it is the GROMacs Pre-Processor that does all such for mdrun. When you get some advice, it's good politics to be seen to follow those up (or reject with reasons) before casting about wildly with other theories :-) You don't want the people giving free advice feeling like you're wasting their time! Mark On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- I'd say it's evident that if the file is not corrupted (use gmxcheck), the GROMACS installations weren't the same (unmodified) version. Reproduce the conditions and run grompp -h to inspect the version. Perhaps you are having a problem with a shared-library mismatch. If you have such an old version of GROMACS around, either uninstall it and retire the sysadmin, or send the computer to a museum :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] tpr older version message
Hi Marc, I figured it out. I tried upir suggestion and tested the gmxcheck but got the following errors gmxcheck.exe -s1 topol.tpr Please give me TWO run input (.tpr/.tpa/.tpb) files or specify the -m flag to generate a methods.tex file gmxcheck.exe -s1 topol.tpr -m --- Program gmxcheck, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- gcq#332: Thanx for Using GROMACS - Have a Nice Day But then decided I need to run the grompp on my clients along with the pre-processing libraries generated by acpypi. Then tested the mdrun on the .tpr this generated. Then it was missing the aminoacids.dat I downloaded it and everything seems to work. I will now make some additional steps on this workflow so this should now work! Thanks again for your help I very much appreciate it. On Sun, Dec 27, 2009 at 7:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: If I preped the tpr using amber forcefields, could that be the reason? No. The mdrun I am using does not have any force field libraries in its directory. That's irrelevant. Only non-mdrun tools care about the contents of $GMXLIB or local force field files. The point of GROMPP is that it is the GROMacs Pre-Processor that does all such for mdrun. When you get some advice, it's good politics to be seen to follow those up (or reject with reasons) before casting about wildly with other theories :-) You don't want the people giving free advice feeling like you're wasting their time! Mark On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- I'd say it's evident that if the file is not corrupted (use gmxcheck), the GROMACS installations weren't the same (unmodified) version. Reproduce the conditions and run grompp -h to inspect the version. Perhaps you are having a problem with a shared-library mismatch. If you have such an old version of GROMACS around, either uninstall it and retire the sysadmin, or send the computer to a museum :-) Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.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/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/mailing_lists/users.php
Re: [gmx-users] tpr older version message
Jack Shultz wrote: Hi Marc, I figured it out. I tried upir suggestion and tested the gmxcheck but got the following errors gmxcheck.exe -s1 topol.tpr Please give me TWO run input (.tpr/.tpa/.tpb) files or specify the -m flag to generate a methods.tex file gmxcheck.exe -s1 topol.tpr -m --- Program gmxcheck, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- gmxcheck -c is the appropriate usage for checking the contents of a single .tpr file. Using -s1 implies -s2, per the documentation. -Justin gcq#332: Thanx for Using GROMACS - Have a Nice Day But then decided I need to run the grompp on my clients along with the pre-processing libraries generated by acpypi. Then tested the mdrun on the .tpr this generated. Then it was missing the aminoacids.dat I downloaded it and everything seems to work. I will now make some additional steps on this workflow so this should now work! Thanks again for your help I very much appreciate it. On Sun, Dec 27, 2009 at 7:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: If I preped the tpr using amber forcefields, could that be the reason? No. The mdrun I am using does not have any force field libraries in its directory. That's irrelevant. Only non-mdrun tools care about the contents of $GMXLIB or local force field files. The point of GROMPP is that it is the GROMacs Pre-Processor that does all such for mdrun. When you get some advice, it's good politics to be seen to follow those up (or reject with reasons) before casting about wildly with other theories :-) You don't want the people giving free advice feeling like you're wasting their time! Mark On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I preped this ligand using acpypi followed by grompp grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top I tested this .tpr file on my server. WheI had another computer run it I get the following message. However we are using the same versions of gromacs. Back Off! I just backed up md.log to ./#md.log.2# --- Program mdrun, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible --- I'd say it's evident that if the file is not corrupted (use gmxcheck), the GROMACS installations weren't the same (unmodified) version. Reproduce the conditions and run grompp -h to inspect the version. Perhaps you are having a problem with a shared-library mismatch. If you have such an old version of GROMACS around, either uninstall it and retire the sysadmin, or send the computer to a museum :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] convert B-factor
Dear all, I want to convert the difference of two rmsf data sets into B-factor of a coordinate (to illustrate their difference by coloring the structure by B-factor), can anyone tell me how to do it? Thanks in advance! Antonio-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] convert B-factor
AntonioLeung wrote: Dear all, I want to convert the difference of two rmsf data sets into B-factor of a coordinate (to illustrate their difference by coloring the structure by B-factor), can anyone tell me how to do it? g_rmsf -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD on more than 64 processors
On Mon, 28 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos - REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the system at respective temperatures (total of 35 equilibration simulations). After this I generated chk_0.tpr, chk_1.tpr, ..., chk_34.tpr files from the equilibrated structures. Now when I submit final job for REMD with following command-line, itgives some error: command line: mpiexec -np 70 mdrun -multi 35 -replex 1000 -s chk_.tpr-v error msg: --- Program mdrun_mpi, VERSION 4.0.7 Source code file: ../../../SRC/src/gmxlib/smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0x9a400030 (called from file ../../../SRC/src/mdlib/ns.c, line 503) --- Thanx for Using GROMACS - Have a Nice Day :Cannot allocate memory Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 19 out of 70 *** The individual node on the cluster has 8GB of physical memory and 16GBof swap memory. Moreover, when logged onto the individual nodes, it shows more than 1GB of free memory, so there should be no problem with cluster memory. Also, the equilibration jobs for the same system are run on the same cluster without any problem. What I have observed by submitting different test jobs with varying number of processors (and no. of replicas, wherever necessary), that any jobwith total number of processors = 64, runs faithfully without any problem.As soon as total number of processors are more than 64, it gives the above error. I have tested this with 65 processors/65 replicas also. This sounds like you might be running on fewer physical CPUs than you have available. If so, running multiple MPI processes per physical CPU can lead to memory shortage conditions. I don't understand what you mean. Do you mean, there might be more than 8 processes running per node (each node has 8 processors)? But that also does not seem to be the case, as SGE (sun grid engine) output shows only eight processes per node. 65 processes can't have 8 processes per node. why can't it have? as i said, there are 8 processors per node. what i have not mentioned is that how many nodes it is using. The jobs got distributed over 9 nodes. 8 of which corresponds to 64 processors + 1 processor from 9th node. OK, that's a full description. Your symptoms are indicative of someone making an error somewhere. Since GROMACS works over more than 64 processors elsewhere, the presumption is that you are doing something wrong or the machine is not set up in the way you think it is or should be. To get the most effective help, you need to be sure you're providing full information - else we can't tell which error you're making or (potentially) eliminate you as a source of error. Sorry for not being clear in statements. As far I can tell you, job distribution seems okay to me. It is 1 job per processor. Does non-REMD GROMACS run on more than 64 processors? Does your cluster support using more than 8 nodes in a run? Can you run an MPI Hello world application that prints the processor and node ID across more than 64 processors? Yes, the cluster supports runs with more than 8 nodes. I generated a system with 10 nm water box and submitted on 80 processors. It was running fine. It printed all 80 NODEIDs. Also showed me when the job will get over. bharat Mark bharat Mark I don't know what you mean by swap memory. Sorry, I meant cache memory.. bharat Mark System: Protein + water + Na ions (total 46878 atoms) Gromacs version: tested with both v4.0.5 and v4.0.7 compiled with: --enable-float --with-fft=fftw3 --enable-mpi compiler: gcc_3.4.6 -O3 machine details: uname -mpio: x86_64 x86_64 x86_64 GNU/Linux I tried searching the mailing-list without any luck. I am not sure, ifi am doing anything wrong in giving commands. Please correct me if it is wrong. Kindly let me know the solution.
Re: [gmx-users] convert B-factor
I know how to calculate, and have calculated the RMSF of two trajectories (of the same molecule), and I want to compare the two RMSFs. I want convert their discrepancy into B-factors. Can you tell me more detailed? -- Original -- From: Mark Abrahammark.abra...@anu.edu.au; Date: Mon, Dec 28, 2009 11:04 AM To: Discussion list for GROMACS usersgmx-users@gromacs.org; Subject: Re: [gmx-users] convert B-factor AntonioLeung wrote: Dear all, I want to convert the difference of two rmsf data sets into B-factor of a coordinate (to illustrate their difference by coloring the structure by B-factor), can anyone tell me how to do it? g_rmsf -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] protein simulation
Dear all, I am trying to do a simulation of protein OMPA. At the step grompp, it shows a fatal error stated Fatal error: Atomtype 'HC' not found! I tried to configure the error but i failed. So, hope that anyone can help me in this. Thnaks.. _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Replica Exchange MD on more than 64 processors
bharat v. adkar wrote: On Mon, 28 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos - REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the systemat respective temperatures (total of 35 equilibration simulations). After this I generated chk_0.tpr, chk_1.tpr, ..., chk_34.tpr filesfrom the equilibrated structures. Now when I submit final job for REMD with following command-line, itgives some error: command line: mpiexec -np 70 mdrun -multi 35 -replex 1000 -schk_.tpr-v error msg: --- Program mdrun_mpi, VERSION 4.0.7 Source code file: ../../../SRC/src/gmxlib/smalloc.c, line: 179 Fatal error: Not enough memory. Failed to realloc 790760 bytes for nlist-jjnr, nlist-jjnr=0x9a400030 (called from file ../../../SRC/src/mdlib/ns.c, line 503) --- Thanx for Using GROMACS - Have a Nice Day :Cannot allocate memory Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 19 out of 70 *** The individual node on the cluster has 8GB of physicalmemory and 16GBof swap memory. Moreover, when logged onto the individual nodes, it shows more than 1GB of free memory, so there should be no problem with cluster memory. Also, the equilibration jobs for the same system arerun on the same cluster without any problem. What I have observed by submitting different test jobs with varying number of processors (and no. of replicas, wherever necessary), thatany jobwith total number of processors = 64, runs faithfully without anyproblem.As soon as total number of processors are more than 64, it gives the above error. I have tested this with 65 processors/65 replicas also. This sounds like you might be running on fewer physical CPUsthan you have available. If so, running multiple MPI processes perphysical CPU can lead to memory shortage conditions. I don't understand what you mean. Do you mean, there might be morethan 8 processes running per node (each node has 8 processors)? But that also does not seem to be the case, as SGE (sun grid engine) output showsonly eight processes per node. 65 processes can't have 8 processes per node. why can't it have? as i said, there are 8 processors per node. what i have not mentioned is that how many nodes it is using. The jobs got distributed over 9 nodes. 8 of which corresponds to 64 processors + 1 processor from 9th node. OK, that's a full description. Your symptoms are indicative of someone making an error somewhere. Since GROMACS works over more than 64 processors elsewhere, the presumption is that you are doing something wrong or the machine is not set up in the way you think it is or should be. To get the most effective help, you need to be sure you're providing full information - else we can't tell which error you're making or (potentially) eliminate you as a source of error. Sorry for not being clear in statements. As far I can tell you, job distribution seems okay to me. It is 1 job per processor. Does non-REMD GROMACS run on more than 64 processors? Does your cluster support using more than 8 nodes in a run? Can you run an MPI Hello world application that prints the processor and node ID across more than 64 processors? Yes, the cluster supports runs with more than 8 nodes. I generated a system with 10 nm water box and submitted on 80 processors. It was running fine. It printed all 80 NODEIDs. Also showed me when the job will get over. bharat Mark bharat Mark I don't know what you mean by swap memory. Sorry, I meant cache memory.. bharat Mark System: Protein + water + Na ions (total 46878 atoms) Gromacs version: tested with both v4.0.5 and v4.0.7 compiled with: --enable-float --with-fft=fftw3 --enable-mpi compiler: gcc_3.4.6 -O3 machine details: uname -mpio: x86_64 x86_64 x86_64 GNU/Linux I tried searching the mailing-list without any luck. Iam not sure, ifi am doing anything wrong in giving commands. Please correct meif it is wrong. Kindly let me
