Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan@aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan@aecom.yu.edu
On Fri, 27 Jun 2008, Dong-Yan Tan wrote:
Dear all,
We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot.
Dong-Yan
This sounds like a Linux kernel bug or C library bug. Please make sure that you have applied all of the recommended patches to your SUSE system (use the yast program to update it). In particular, there is a security patch related to floating point exceptions, that should be applied (<http://www.novell.com/linux/security/advisories/2004_17_kernel.html>). It's not clear if that patch will fix the problem, so please apply the rest. I would also expect upgrading to the current SUSE Linux to fix the problem. Good luck, Greg Couch UCSF Computer Graphics Lab
I would also expect upgrading to the current SUSE Linux to fix the problem.
One thing (not particularly related to Chimera) that is preventing us to upgrade the system, is the risk of breaking other programs. In a particular the newer versions of Linux come without G77 (Fortran 77 compiler) and come with the newer "better" G90 compiler. I suspect a big headache when trying to compile old Fortran coded programs that we still use. Greg Couch wrote:
On Fri, 27 Jun 2008, Dong-Yan Tan wrote:
Dear all,
We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot.
Dong-Yan
This sounds like a Linux kernel bug or C library bug. Please make sure that you have applied all of the recommended patches to your SUSE system (use the yast program to update it). In particular, there is a security patch related to floating point exceptions, that should be applied (<http://www.novell.com/linux/security/advisories/2004_17_kernel.html>). It's not clear if that patch will fix the problem, so please apply the rest.
I would also expect upgrading to the current SUSE Linux to fix the problem.
Good luck,
Greg Couch UCSF Computer Graphics Lab _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
We compile a little bit of fortran code for chimera, and so far, we have not had any problems substituting gfortran for g77. But I understand your reluctance. For chimera, we use a newer version of gcc than what comes with the system by compiling our own from source and giving the "--prefix=/home/chimera" configuration option. Then users, who wish to use that compiler, put ~chimera/bin into the PATH environment variable and ~chimera/lib into the LD_LIBRARY_PATH environment variable. You could do something similar to check if the new compiler is really a problem or not before upgrading. You could also upgrade Linux and install an older compiler in a similar fashion. - Greg On Fri, 27 Jun 2008, hsosa@aecom.yu.edu wrote:
I would also expect upgrading to the current SUSE Linux to fix the problem.
One thing (not particularly related to Chimera) that is preventing us to upgrade the system, is the risk of breaking other programs. In a particular the newer versions of Linux come without G77 (Fortran 77 compiler) and come with the newer "better" G90 compiler. I suspect a big headache when trying to compile old Fortran coded programs that we still use.
Greg Couch wrote:
On Fri, 27 Jun 2008, Dong-Yan Tan wrote:
Dear all,
We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot.
Dong-Yan
This sounds like a Linux kernel bug or C library bug. Please make sure that you have applied all of the recommended patches to your SUSE system (use the yast program to update it). In particular, there is a security patch related to floating point exceptions, that should be applied (<http://www.novell.com/linux/security/advisories/2004_17_kernel.html>). It's not clear if that patch will fix the problem, so please apply the rest.
I would also expect upgrading to the current SUSE Linux to fix the problem.
Good luck,
Greg Couch UCSF Computer Graphics Lab _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
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