Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz
Dear colleagues, thanks to all of you who replied to my post. Thanks specially to Peter, who was spot on with finding the cause of the problem - the missing version statement in libgfortran.so.3, and to Marcin, who posted the workaround (ln -s libgfortran.so.3.0.0 $CCP4/lib/libgfortran.so.3). It seems to work for now (Refmac is running again), and perhaps the next update will address this. Cheers, Merry Christmas Happy New Year, Uli _ dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrueck-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de
Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz
Dear Partha and Uli, We haven't tested it on SLES11 and we overlooked this problem. It will be fixed in updates. For now as a workaround do: ln -s libgfortran.so.3.0.0 $CCP4/lib/libgfortran.so.3 (hopefully works, I cannot test it now) Usually the quickest way to have such problems solved is to email CCP4 helpdesk (c...@ccp4.ac.uk). Marcin On Mon, Dec 16, 2013 at 12:53:58PM -0500, Parthasarathy Sampathkumar wrote: Yes Uli. I have the same issue, but not solve it yet :-( Partha On Mon, Dec 16, 2013 at 10:52 AM, ulrich.goh...@mdc-berlin.de ulrich.goh...@mdc-berlin.de wrote: Dear colleagues, Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the following error when I fill in the file box for the data file: CCP4i encountered an error when trying to extract the data from data.mtz. You can view the output from the mtzdump program etc. + crash of the GUI. Now, running mtzdump gives me this: http://www.hkl-xray.com/data-upload-form-and-bug-report./mtzdump: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.1' not found (required by /xprogs/CCP4/CCP4-6.4.0/destination/ccp4-6.4.0/bin/../lib/libccp4f.so.0) In /usr/lib64 I have softlinked libgfortran.so.3 - libgfortran.so.3.0.0 (did so in 2011). I am not sure what I need to update here and how. I am running Novell's SLES 11 on a 64 bit system with the libgfortran43 runtime library installed. I have also checked file permissions (incl. tmp directories), and I cannot find anything obvious. I cannot remember having had similar problems with v6.3.0 in the beginning. Has anyone encountered the same problem and solved it yet? My apologies if this has been discussed already; I searched the archive and I couldn't find a similar thread. Cheers, Uli --- dr ulrich gohlke *staff scientist - m**acromolecular structure and interaction* max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/ -- Scanned by iCritical.
Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz
Dear Uli, On Mon, 2013-12-16 at 15:52 +, ulrich.goh...@mdc-berlin.de wrote: Dear colleagues, Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the following error when I fill in the file box for the data file: CCP4i encountered an error when trying to extract the data from data.mtz. You can view the output from the mtzdump program etc. + crash of the GUI. Now, running mtzdump gives me this: ./mtzdump: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.1' not found (required by /xprogs/CCP4/CCP4-6.4.0/destination/ccp4-6.4.0/bin/../lib/libccp4f.so.0) In /usr/lib64 I have softlinked libgfortran.so.3 - libgfortran.so.3.0.0 (did so in 2011). I am not sure what I need to update here and how. I am running Novell's SLES 11 on a 64 bit system with the libgfortran43 runtime library installed. I have also checked file permissions (incl. tmp directories), and I cannot find anything obvious. I cannot remember having had similar problems with v6.3.0 in the beginning. This may be a problem with the version information in the gfortran library supplied by SUSE not containing anything matching the version used by CCP4 on the system that they use for building their binaries. For more information, you could try the commands: ldd -v /path/to/mtzdump which will list explicitly the version information of the required shared libraries, and: readelf -V /usr/lib64/libgfortran.so.3 and looking for the section starting Version definition section: it should look something like this: Version definition section '.gnu.version_d' contains 9 entries: Addr: 0x00015da0 Offset: 0x015da0 Link: 5 (.dynstr) 00: Rev: 1 Flags: BASE Index: 1 Cnt: 1 Name: libgfortran.so.3 0x001c: Rev: 1 Flags: none Index: 2 Cnt: 1 Name: GFORTRAN_1.0 0x0038: Rev: 1 Flags: none Index: 3 Cnt: 2 Name: GFORTRAN_1.1 0x0054: Parent 1: GFORTRAN_1.0 0x005c: Rev: 1 Flags: none Index: 4 Cnt: 2 Name: GFORTRAN_1.2 0x0078: Parent 1: GFORTRAN_1.1 0x0080: Rev: 1 Flags: none Index: 5 Cnt: 2 Name: GFORTRAN_1.3 0x009c: Parent 1: GFORTRAN_1.2 0x00a4: Rev: 1 Flags: none Index: 6 Cnt: 2 Name: GFORTRAN_1.4 0x00c0: Parent 1: GFORTRAN_1.3 0x00c8: Rev: 1 Flags: none Index: 7 Cnt: 1 Name: F2C_1.0 0x00e4: Rev: 1 Flags: none Index: 8 Cnt: 1 Name: GFORTRAN_C99_1.0 0x0100: Rev: 1 Flags: none Index: 9 Cnt: 2 Name: GFORTRAN_C99_1.1 0x011c: Parent 1: GFORTRAN_C99_1.0 I suspect that your version may be missing the GFORTRAN_1.1 entry (the above listing is from openSUSE 12.3, which does have the correct version). If so, maybe this is something that CCP4 need to deal with in their build of the official binaries. Alternatively, if you build CCP4 from source on your system, it should work. Has anyone encountered the same problem and solved it yet? We have a SLES licence at Global Phasing, although we haven't run CCP4 on a SLES system for a long time now. Your experience suggests that we should give it a try again: we had been assuming that if it works with openSUSE then SLES/SLED should also be OK but now it seems not :-) I'm afraid that I am unlikely to have time to do this before January though, so it won't help you if you are in a hurry. Unless someone else who is running CCP4 under SLES has a quick fix, I think that building CCP4 from source may be your quickest solution. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz
Yes Uli. I have the same issue, but not solve it yet :-( Partha On Mon, Dec 16, 2013 at 10:52 AM, ulrich.goh...@mdc-berlin.de ulrich.goh...@mdc-berlin.de wrote: Dear colleagues, Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the following error when I fill in the file box for the data file: CCP4i encountered an error when trying to extract the data from data.mtz. You can view the output from the mtzdump program etc. + crash of the GUI. Now, running mtzdump gives me this: http://www.hkl-xray.com/data-upload-form-and-bug-report./mtzdump: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.1' not found (required by /xprogs/CCP4/CCP4-6.4.0/destination/ccp4-6.4.0/bin/../lib/libccp4f.so.0) In /usr/lib64 I have softlinked libgfortran.so.3 - libgfortran.so.3.0.0 (did so in 2011). I am not sure what I need to update here and how. I am running Novell's SLES 11 on a 64 bit system with the libgfortran43 runtime library installed. I have also checked file permissions (incl. tmp directories), and I cannot find anything obvious. I cannot remember having had similar problems with v6.3.0 in the beginning. Has anyone encountered the same problem and solved it yet? My apologies if this has been discussed already; I searched the archive and I couldn't find a similar thread. Cheers, Uli --- dr ulrich gohlke *staff scientist - m**acromolecular structure and interaction* max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
