Re: [gmx-users] Double precision test failure
Berk Hess wrote: Ah, this could be the issue. Depending on how you configure the double precision binaries could have the same names as the single precision ones, or they could have _d appended. I guess the test scripts can not figure out what they should use, but currently they apparently request the _d appended names. That's correct. In addition I think that we should start distributing packages that contain both single and double precision binaries. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double precision test failure
Ah, this could be the issue. Depending on how you configure the double precision binaries could have the same names as the single precision ones, or they could have _d appended. I guess the test scripts can not figure out what they should use, but currently they apparently request the _d appended names. Berk. From: Chris Snook <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Double precision test failure Date: Fri, 30 Nov 2007 08:20:11 -0500 The gromacs commands are in my search path as both the commands suggested worked. The single precision tests worked but it was the double precision tests that completely failed. All of the grompp.out files contain the single line error : sh: line 1: grompp_d: command not found Checking the bin directory, indeed there is no grompp_d binary. Was the Mac OS X binaries only compiled for single precision? Chris David van der Spoel wrote: Chris Snook wrote: Yes, The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly defined whether I use sh or bash as the shell. I do get the following errors when I run GMXRC in either shell: ../bin/GMXRC: line 35: return: can only `return' from a function or sourced script ../bin/GMXRC: line 44: CSH:: command not found ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""' you should in sh or bash type . GMXRC the important question is whether the gromacs commands are in your search path. this is best test by typing grompp -h or luck If they are there then something else is wrong in the test set. Please check the grompp.out files in the subdirectories. Regards Chris Quoting David van der Spoel <[EMAIL PROTECTED]>: Chris Snook wrote: I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. did you source GMXRC? Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- *** Chris F. Snook, Ph.D. X-ray Crystallography Core Manager Dept. of Biochemistry & Molecular Biology Medical University of South Carolina 173 Ashley Avenue Charleston SC 29425 USA Phone: 843-792-5848 FAX:843-792-4322 email: [EMAIL PROTECTED] *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 sen
Re: [gmx-users] Double precision test failure
The gromacs commands are in my search path as both the commands suggested worked. The single precision tests worked but it was the double precision tests that completely failed. All of the grompp.out files contain the single line error : sh: line 1: grompp_d: command not found Checking the bin directory, indeed there is no grompp_d binary. Was the Mac OS X binaries only compiled for single precision? Chris David van der Spoel wrote: Chris Snook wrote: Yes, The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly defined whether I use sh or bash as the shell. I do get the following errors when I run GMXRC in either shell: ../bin/GMXRC: line 35: return: can only `return' from a function or sourced script ../bin/GMXRC: line 44: CSH:: command not found ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""' you should in sh or bash type . GMXRC the important question is whether the gromacs commands are in your search path. this is best test by typing grompp -h or luck If they are there then something else is wrong in the test set. Please check the grompp.out files in the subdirectories. Regards Chris Quoting David van der Spoel <[EMAIL PROTECTED]>: Chris Snook wrote: I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. did you source GMXRC? Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- *** Chris F. Snook, Ph.D. X-ray Crystallography Core Manager Dept. of Biochemistry & Molecular Biology Medical University of South Carolina 173 Ashley Avenue Charleston SC 29425 USA Phone: 843-792-5848 FAX:843-792-4322 email: [EMAIL PROTECTED] *** ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double precision test failure
Chris Snook wrote: Yes, The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly defined whether I use sh or bash as the shell. I do get the following errors when I run GMXRC in either shell: ../bin/GMXRC: line 35: return: can only `return' from a function or sourced script ../bin/GMXRC: line 44: CSH:: command not found ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""' you should in sh or bash type . GMXRC the important question is whether the gromacs commands are in your search path. this is best test by typing grompp -h or luck If they are there then something else is wrong in the test set. Please check the grompp.out files in the subdirectories. Regards Chris Quoting David van der Spoel <[EMAIL PROTECTED]>: Chris Snook wrote: I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. did you source GMXRC? Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double precision test failure
Yes, The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly defined whether I use sh or bash as the shell. I do get the following errors when I run GMXRC in either shell: ../bin/GMXRC: line 35: return: can only `return' from a function or sourced script ../bin/GMXRC: line 44: CSH:: command not found ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' ../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""' Regards Chris Quoting David van der Spoel <[EMAIL PROTECTED]>: Chris Snook wrote: I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. did you source GMXRC? Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double precision test failure
Chris Snook wrote: I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. did you source GMXRC? Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Double precision test failure
I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
