RE: [gmx-users] gromacs on glacier
Hi Justin, Regarding your suggestion using spc216, when I tried the energetically minimize spc216 with grompp,I got the following error: Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype Same thing happened when I tried TIP4P. Where is the problem? I did not have this issue with my own model. Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 1:53 PM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Well, I think that MPICH is your problem then. There are several reports of sporadic bugs (the one that you're seeing!) with that version. Since it's several years old, getting a fix is probably a bit unlikely :) Perhaps you can sort out with the sysadmins what you can do. Like I said before, probably OpenMPI is a better bet - we've never had a problem with it. You can probably install it yourself in your home directory, and point to mpicc with environment variables during the Gromacs installation. Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Probably not a very good test case for diagnosing problems, but I think it's unrelated in this case. When testing, keep it simple - run a simulation with spc216.gro from the Gromacs installation, it should pretty much always work :) -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7.make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip
Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote: Hi Justin, Regarding your suggestion using spc216, when I tried the energetically minimize spc216 with grompp,I got the following error: Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype Same thing happened when I tried TIP4P. Where is the problem? I did not have this issue with my own model. Something is malformed in your .top, but it's impossible to comment any further unless you post your entire .top file. -Justin Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 1:53 PM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Well, I think that MPICH is your problem then. There are several reports of sporadic bugs (the one that you're seeing!) with that version. Since it's several years old, getting a fix is probably a bit unlikely :) Perhaps you can sort out with the sysadmins what you can do. Like I said before, probably OpenMPI is a better bet - we've never had a problem with it. You can probably install it yourself in your home directory, and point to mpicc with environment variables during the Gromacs installation. Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Probably not a very good test case for diagnosing problems, but I think it's unrelated in this case. When testing, keep it simple - run a simulation with spc216.gro from the Gromacs installation, it should pretty much always work :) -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message
Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, … it will crash. Following are the last lines reported in different files: “In the log file of the code”: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ 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 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
RE: [gmx-users] gromacs on glacier
Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ 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 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 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] gromacs on glacier
Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ 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 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
RE: [gmx-users] gromacs on glacier
Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1../configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2.Make 3.Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4.Make clean This command will clean some files generated during installation which are not needed anymore. 5../configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6.make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8.Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ 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 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
Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote: Dear Justin, Here is the mpich version: MPICH Version: 1.2.7p1 MPICH Release date: $Date: 2005/11/04 11:54:51$ MPICH Patches applied: none MPICH configure:-prefix=/share/apps/intel/mpich/ MPICH Device: ch_p4 Well, I think that MPICH is your problem then. There are several reports of sporadic bugs (the one that you're seeing!) with that version. Since it's several years old, getting a fix is probably a bit unlikely :) Perhaps you can sort out with the sysadmins what you can do. Like I said before, probably OpenMPI is a better bet - we've never had a problem with it. You can probably install it yourself in your home directory, and point to mpicc with environment variables during the Gromacs installation. Also the gcc compiler: gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) Copyright (C) 2006 Free Software Foundation, Inc. About the system, I have water model with 3 atom sites and 3 virtual sites. Probably not a very good test case for diagnosing problems, but I think it's unrelated in this case. When testing, keep it simple - run a simulation with spc216.gro from the Gromacs installation, it should pretty much always work :) -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well): Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. This is pretty much the standard installation procedure. What we also need to know are the compilers used, etc. for the installation. The error you're getting is from MPICH. Which version is installed on the cluster? It may be old and buggy. In any case, you can try to install something newer, like a recent version of OpenMPI (which we have on our cluster); it may be more reliable. Only a random thought, means nothing unless we know what you have installed :) What about the contents of your system, as I asked before? Do you really have a 100% virtual site system? -Justin Sorry for tons of e-mails. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: In the log file of the code: There are: 1611 Atoms There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: p2_22627: p4_error: Timeout in establishing connection to remote process: 0 This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html snip To me, it seems that code can not communicate through more than one node. I am suspicious of doing sth wrong during installation! I tried wiki, but I can not find the documents as before, and I eally do not know in which step I might have gone wrong. If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin Payman ___ gmx-users mailing list
