Dear Uli, On Mon, 2013-12-16 at 15:52 +0000, [email protected] 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: 0x0000000000015da0 Offset: 0x015da0 Link: 5 (.dynstr) > 000000: 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
