Re: [ccp4bb] HKL2000 and gcc4 - redux
Hi, On Thu, 8 May 2008, James Stroud wrote: On May 7, 2008, at 3:07 PM, Chris Waddling wrote: so even temporarily putting a library where it doesn't belong Actually, this is what /usr/lib is for (except for the doesn't part). According to the Filesystem Hierarchy Standard 4.7 regarding the general requirements and limitations of files placed in /usr/lib: /usr/lib includes object files, libraries, and internal binaries that are not intended to be executed directly by users or shell scripts. If it fulfills the definition and is not expressly forbidden, then its reasonable to assume its allowed. The issue here is not _what_ certain directories contain, but _how_ the contents of those directories are maintained, and the FHS has nothing to say about that. In most distributions, /usr/lib will be one of the directories maintained by the system's software packaging mechanism (zypper, rug, dpkg, or whatever). You would be well advised not to put files willy-nilly into it. I can expand on this if anyone who doesn't already know is interested. Whenever someone finds themselves wanting to put a file in a directory like /usr/bin, /usr/lib, /sbin etc., there will almost always be a better way, as indeed this thread has shown. Regards, Peter.
Re: [ccp4bb] HKL2000 and gcc4 - redux
On May 7, 2008, at 3:07 PM, Chris Waddling wrote: so even temporarily putting a library where it doesn't belong Actually, this is what /usr/lib is for (except for the doesn't part). According to the Filesystem Hierarchy Standard 4.7 regarding the general requirements and limitations of files placed in /usr/lib: /usr/lib includes object files, libraries, and internal binaries that are not intended to be executed directly by users or shell scripts. If it fulfills the definition and is not expressly forbidden, then its reasonable to assume its allowed. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] HKL2000 and gcc4 - redux
mosflm is an incredibly great program, not to mention free as in beer... On May 7, 2008, at 3:07 PM, Chris Waddling wrote: my frustration at HKL2000 not working
Re: [ccp4bb] HKL2000 and gcc4 - redux
Dear Chris, Bill just beat me to writing the same. I would mention XDS as well. With best wishes, Gerard. -- On Wed, May 07, 2008 at 03:17:07PM -0700, William Scott wrote: mosflm is an incredibly great program, not to mention free as in beer... On May 7, 2008, at 3:07 PM, Chris Waddling wrote: my frustration at HKL2000 not working -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] HKL2000 and gcc4 - redux
Agreed, but it's nice to have options, as I'm sure we've all experienced, one program (and sometimes it's HKL2000) just seems to work better than another with some data. But yes, being that this is the CCP4BB, mosflm does indeed rock. Thanks, Chris From: Gerard Bricogne [EMAIL PROTECTED] Date: Wed, 7 May 2008 23:23:34 +0100 To: Chris Waddling [EMAIL PROTECTED] Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] HKL2000 and gcc4 - redux Dear Chris, Bill just beat me to writing the same. I would mention XDS as well. With best wishes, Gerard. -- On Wed, May 07, 2008 at 03:17:07PM -0700, William Scott wrote: mosflm is an incredibly great program, not to mention free as in beer... On May 7, 2008, at 3:07 PM, Chris Waddling wrote: my frustration at HKL2000 not working -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] HKL2000 and gcc4
Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling
Re: [ccp4bb] HKL2000 and gcc4
Get a new sys-admin. He is getting in the way of your research. There is no good reason to be paranoid about this particular shared library sitting in /usr/lib. James On May 5, 2008, at 1:32 PM, Chris Waddling wrote: I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] HKL2000 and gcc4
Chris Waddling wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling Have you installed the compatibility libraries compat-libstdc++-33 and libstdc++296? This is easily accomplished using yum if it is installed, e.g., $ yum -y install compat-libstdc++-33 compat-libstdc++-296 These libraries are required for programs compiled using GCC 3.x Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] HKL2000 and gcc4
On Mon, 05 May 2008 13:48:00 -0600, James Stroud [EMAIL PROTECTED] wrote: Get a new sys-admin. He is getting in the way of your research. There is no good reason to be paranoid about this particular shared library sitting in /usr/lib. James On May 5, 2008, at 1:32 PM, Chris Waddling wrote: I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. I'd echo James, but to say that there is no reason that you cannot have both gcc3 and gcc4 installed. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 [EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc
Re: [ccp4bb] HKL2000 and gcc4
Hi Chris, On Mon, 05 May 2008 12:57:17 -0700, Chris Waddling [EMAIL PROTECTED] wrote: Robert, that's exactly what I keep asking him to do maybe I should take James Stroud's advice... Yes, maybe you should, if you cannot convince him of the error of his ways. :) BTW, nice to hear from my M.Sc. alma mater... I worked in Donal Macarntney's Chemistry lab from '91-93. I haven't crossed paths with Donal, just with a couple of others like Victor Snieckus and David Zechel in the Chemistry department here. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 [EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc
Re: [ccp4bb] HKL2000 and gcc4
Hi, Have you installed the compatibility libraries compat-libstdc++-33 and libstdc++296? This is easily accomplished using yum if it is installed, e.g., $ yum -y install compat-libstdc++-33 compat-libstdc++-296 These libraries are required for programs compiled using GCC 3.x Those packages don't provide libg2c but they are good to have. You need yum install compat-libf2c-34 for libg2c.so.0 assuming you're using RHEL5 or greater. In any case, we're using v0.98.698d and it doesn't seem to need libg2c: % ldd `which hkl2000` linux-gate.so.1 = (0x4000) libX11.so.6 = /usr/lib/libX11.so.6 (0x00ada000) libm.so.6 = /lib/libm.so.6 (0x00a7) libdl.so.2 = /lib/libdl.so.2 (0x00a99000) libc.so.6 = /lib/libc.so.6 (0x0092e000) libXau.so.6 = /usr/lib/libXau.so.6 (0x00acd000) libXdmcp.so.6 = /usr/lib/libXdmcp.so.6 (0x00ad2000) /lib/ld-linux.so.2 (0x0090d000) which version of HKL2000 are you using that requires libg2c?
Re: [ccp4bb] HKL2000 and gcc4
Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This no doubt qualifies as an obvious question, but have you tried /usr/local/lib? That is often automatically searched for libraries on Linux systems, and is often used as a resting place for obsolete libraries for that reason. It's preferable, if they're available for your flavor of Linux, to use compatibility packages as Professor Rowlett mentions. You'll probably need compat-g77, or something similar, as libg2c is the old Fortran compatibility library for GCC. -- Michael Strickler, Ph.D. Research Specialist Center for Structural Biology Yale University 260 Whitney Ave, 355C JWG PO Box 208114 New Haven, CT 06520-8114
Re: [ccp4bb] HKL2000 and gcc4
On ubuntu, you can get this in the libg2c package. I agree with James Stroud. Fire the sysadmin and divvy the salary up amongst those who really need it. Time to raise the black flag and start slitting throats. On May 5, 2008, at 12:32 PM, Chris Waddling wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling
Re: [ccp4bb] HKL2000 and gcc4
I had similar problem with Mosflm due to odd combination of Suse and AMD-64. Copied those files from a different installation, everything runs just fine.. would agree with James.. lol.. On Mon, May 5, 2008 at 8:32 PM, Chris Waddling [EMAIL PROTECTED] wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] HKL2000 and gcc4
Thanks all for your suggestions. It turns out that I was mis-defining the LD_LIBRARY_PATH (using 'set' instead of 'setenv'). Dumb mistake, but thanks to our sysadmin pointing this out, all's good. Chris
