Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Dear Phil, The message indeed relates to picking up the system libc which is too old for the declared dependency in the make scripts. RedHat/CentOS/ScientficLinux are all based on 2.x kernels and upgrading on that path is unlikely to satisfy the dependency. It seems there are three ways around this: 1) Get the version compiled with the lower libc requirement (which begs the question why have the newer one? It was probably just picking up the default) 2) Install a second libc that is newer and privately link it. I don't recommend this as it is long and involved 3) Look at the CERN devtoolset features. This mimics a newer system by statically linking in the required patches to allow you then to link against the older system library. This is the route we use with few problems. There are many reasons to retain older versions of operating systems and kernels. Regards, Robert -- Dr. Robert Esnouf, University Research Lecturer, Head of Research Computing Core, NDM Research Computing Strategy Officer Room 10/028, Wellcome Trust Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK Email: rob...@strubi.ox.ac.uk / rob...@well.ox.ac.uk Tel: (+44) - 1865 - 287783 Original message >Date: Wed, 26 Oct 2016 17:46:15 +0200 >From: CCP4 bulletin board (on behalf of George >Sheldrick ) >Subject: Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS >To: CCP4BB@JISCMAIL.AC.UK > >Dear Kay, > >Exactly. That is why we provided two Linux versions (called pdb2ins and >pdb2ins_oldlinux) on the SHELX server. >So far two versions seem to be enough and for Macs and Windows only one >version seems to be required. If >anyone finds this to be insufficient, please let Anna know giving >details of which OS or Linux distribution you >are using. > >At the moment we are only providing 64-bit versions of pdb2ins and there >have been no complaints about that. >This raises the question of whether I am wasting my time providing both >32- and 64-bit versions of all the SHELX >programs?! > >Best wishes, George >CC Anna > >On 10/26/2016 05:12 PM, Kay Diederichs wrote: >> Hi Phil, >> >> the error message occurs because your glibc is too old for this binary. The >> glibc cannot easily be updated, it is tied to the distribution, in your >> case RHEL6. A newer kernel does not change this, nor would an update to RHEL >> 6.8 >> This is why distributed Linux software should be built on dated >> distributions. >> >> Best, >> >> Kay >> >> On Wed, 26 Oct 2016 12:11:25 +0100, Phil Evans >> wrote: >> >>> Hi George >>> >>> I�m not sure that anyone here is using shelxl but I�ve just updated our >>> general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I >>> get a complaint. Do you understand this? (I should probably ask our local >>> guys) >>> >>> Our system is >>> Scientific Linux release 6.7 (Carbon) >>> >>> ./pdb2ins >>> ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by >>> /tmp/_MEIQO85tj/libz.so.1) >>> >>> best wishes >>> Phil >>> >>> >>>> On 25 Oct 2016, at 20:31, George Sheldrick >>>> wrote: >>>> >>>> SHELXL may be used to refine both small and macromolecular structures >>>> against X-ray or neutron diffraction data, including non-merohedral twins. >>>> A new version 2016/6 of SHELXL may now be downloaded from the SHELX >>>> server. It has been well tested by about 20 volunteers to whom I am very >>>> grateful. A new version of Anna Luebben's program PDB2INS is also >>>> available there (for 64 bit systems only). PDB2INS makes the preparation >>>> of the .ins and .hkl files to run macromolecular SHELXL refinements much >>>> easier. For most structures deposited in the PDB since 2008 these two >>>> files can be generated automatically and no changes are needed to run >>>> SHELXL. >>>> >>>> George >>>> -- >>>> Prof. George M. Sheldrick FRS >>>> Dept. Structural Chemistry, >>>> University of Goettingen, >>>> Tammannstr. 4, >>>> D37077 Goettingen, Germany >>>> Tel. +49-551-39-33021 or -33068 >>>> Fax. +49-551-39-22582 >>>> >>>> > > >-- >Prof. George M. Sheldrick FRS >Dept. Structural Chemistry, >University of Goettingen, >Tammannstr. 4, >D37077 Goettingen, Germany >Tel. +49-551-39-33021 or -33068 >Fax. +49-551-39-22582
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Dear Kay, Exactly. That is why we provided two Linux versions (called pdb2ins and pdb2ins_oldlinux) on the SHELX server. So far two versions seem to be enough and for Macs and Windows only one version seems to be required. If anyone finds this to be insufficient, please let Anna know giving details of which OS or Linux distribution you are using. At the moment we are only providing 64-bit versions of pdb2ins and there have been no complaints about that. This raises the question of whether I am wasting my time providing both 32- and 64-bit versions of all the SHELX programs?! Best wishes, George CC Anna On 10/26/2016 05:12 PM, Kay Diederichs wrote: Hi Phil, the error message occurs because your glibc is too old for this binary. The glibc cannot easily be updated, it is tied to the distribution, in your case RHEL6. A newer kernel does not change this, nor would an update to RHEL 6.8 This is why distributed Linux software should be built on dated distributions. Best, Kay On Wed, 26 Oct 2016 12:11:25 +0100, Phil Evans wrote: Hi George I�m not sure that anyone here is using shelxl but I�ve just updated our general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a complaint. Do you understand this? (I should probably ask our local guys) Our system is Scientific Linux release 6.7 (Carbon) ./pdb2ins ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIQO85tj/libz.so.1) best wishes Phil On 25 Oct 2016, at 20:31, George Sheldrick wrote: SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very grateful. A new version of Anna Luebben's program PDB2INS is also available there (for 64 bit systems only). PDB2INS makes the preparation of the .ins and .hkl files to run macromolecular SHELXL refinements much easier. For most structures deposited in the PDB since 2008 these two files can be generated automatically and no changes are needed to run SHELXL. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
In line with Kay's message this sounds like pdb2ins having being linked statically with glibc. AFAIK this can be problematic since glibc in reality can never be completely statically linked. This may cause version conflicts if the same version of glibc is not present on the users system. To avoid this problem do not link glibc statically into a binary for distribution. Correct me if I'm wrong. Rob On 26/10/2016 12:11, Phil Evans wrote: Hi George I’m not sure that anyone here is using shelxl but I’ve just updated our general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a complaint. Do you understand this? (I should probably ask our local guys) Our system is Scientific Linux release 6.7 (Carbon) ./pdb2ins ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIQO85tj/libz.so.1) best wishes Phil On 25 Oct 2016, at 20:31, George Sheldrick wrote: SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very grateful. A new version of Anna Luebben's program PDB2INS is also available there (for 64 bit systems only). PDB2INS makes the preparation of the .ins and .hkl files to run macromolecular SHELXL refinements much easier. For most structures deposited in the PDB since 2008 these two files can be generated automatically and no changes are needed to run SHELXL. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Hi Phil, the error message occurs because your glibc is too old for this binary. The glibc cannot easily be updated, it is tied to the distribution, in your case RHEL6. A newer kernel does not change this, nor would an update to RHEL 6.8 This is why distributed Linux software should be built on dated distributions. Best, Kay On Wed, 26 Oct 2016 12:11:25 +0100, Phil Evans wrote: >Hi George > >I�m not sure that anyone here is using shelxl but I�ve just updated our >general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get >a complaint. Do you understand this? (I should probably ask our local guys) > >Our system is >Scientific Linux release 6.7 (Carbon) > > ./pdb2ins >./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by >/tmp/_MEIQO85tj/libz.so.1) > >best wishes >Phil > > >> On 25 Oct 2016, at 20:31, George Sheldrick >> wrote: >> >> SHELXL may be used to refine both small and macromolecular structures >> against X-ray or neutron diffraction data, including non-merohedral twins. A >> new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It >> has been well tested by about 20 volunteers to whom I am very grateful. A >> new version of Anna Luebben's program PDB2INS is also available there (for >> 64 bit systems only). PDB2INS makes the preparation of the .ins and .hkl >> files to run macromolecular SHELXL refinements much easier. For most >> structures deposited in the PDB since 2008 these two files can be generated >> automatically and no changes are needed to run SHELXL. >> >> George >> -- >> Prof. George M. Sheldrick FRS >> Dept. Structural Chemistry, >> University of Goettingen, >> Tammannstr. 4, >> D37077 Goettingen, Germany >> Tel. +49-551-39-33021 or -33068 >> Fax. +49-551-39-22582 >> >>
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Dear Phil, as far as I understand, SL version 6 builds on kernel 2.6.32, which was released nearly a decade ago. Maybe it's time to update? Even the rather conservative Debian stable uses 3.16 ... Best, Tim On Wednesday, October 26, 2016 12:11:25 PM Phil Evans wrote: > Hi George > > I’m not sure that anyone here is using shelxl but I’ve just updated our > general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I > get a complaint. Do you understand this? (I should probably ask our local > guys) > > Our system is > Scientific Linux release 6.7 (Carbon) > > ./pdb2ins > ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by > /tmp/_MEIQO85tj/libz.so.1) > > best wishes > Phil > > > On 25 Oct 2016, at 20:31, George Sheldrick > > wrote: > > > > SHELXL may be used to refine both small and macromolecular structures > > against X-ray or neutron diffraction data, including non-merohedral > > twins. A new version 2016/6 of SHELXL may now be downloaded from the > > SHELX server. It has been well tested by about 20 volunteers to whom I am > > very grateful. A new version of Anna Luebben's program PDB2INS is also > > available there (for 64 bit systems only). PDB2INS makes the preparation > > of the .ins and .hkl files to run macromolecular SHELXL refinements much > > easier. For most structures deposited in the PDB since 2008 these two > > files can be generated automatically and no changes are needed to run > > SHELXL. > > > > George > > -- > > Prof. George M. Sheldrick FRS > > Dept. Structural Chemistry, > > University of Goettingen, > > Tammannstr. 4, > > D37077 Goettingen, Germany > > Tel. +49-551-39-33021 or -33068 > > Fax. +49-551-39-22582 -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Dear Phil, Thank you for the information. We made two versions for Linux available; one packaged on an up-to-date Linux computer and one from an 'older' system. Should there be a library problem with the 'linux' version, the 'oldllinux' version could work. best wishes, Anna On 10/26/2016 12:11 PM, Phil Evans wrote: Hi George I’m not sure that anyone here is using shelxl but I’ve just updated our general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a complaint. Do you understand this? (I should probably ask our local guys) Our system is Scientific Linux release 6.7 (Carbon) ./pdb2ins ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIQO85tj/libz.so.1) best wishes Phil On 25 Oct 2016, at 20:31, George Sheldrick wrote: SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very grateful. A new version of Anna Luebben's program PDB2INS is also available there (for 64 bit systems only). PDB2INS makes the preparation of the .ins and .hkl files to run macromolecular SHELXL refinements much easier. For most structures deposited in the PDB since 2008 these two files can be generated automatically and no changes are needed to run SHELXL. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Mac version runs OK! Martin _ Dr. Martin Martinez-Ripoll Research Professor xmar...@iqfr.csic.es Department of Crystallography & Structural Biology www.xtal.iqfr.csic.es www.xtal.iqfr.csic.es/Cristalografia/ Telf.: +34 917459550 Consejo Superior de Investigaciones Científicas Spanish National Research Council -Mensaje original- De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de Phil Evans Enviado el: miércoles, 26 de octubre de 2016 13:11 Para: CCP4BB@JISCMAIL.AC.UK Asunto: Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS Hi George Im not sure that anyone here is using shelxl but Ive just updated our general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a complaint. Do you understand this? (I should probably ask our local guys) Our system is Scientific Linux release 6.7 (Carbon) ./pdb2ins ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIQO85tj/libz.so.1) best wishes Phil > On 25 Oct 2016, at 20:31, George Sheldrick wrote: > > SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very grateful. A new version of Anna Luebben's program PDB2INS is also available there (for 64 bit systems only). PDB2INS makes the preparation of the .ins and .hkl files to run macromolecular SHELXL refinements much easier. For most structures deposited in the PDB since 2008 these two files can be generated automatically and no changes are needed to run SHELXL. > > George > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-33021 or -33068 > Fax. +49-551-39-22582 > >
Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS
Hi George I’m not sure that anyone here is using shelxl but I’ve just updated our general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a complaint. Do you understand this? (I should probably ask our local guys) Our system is Scientific Linux release 6.7 (Carbon) ./pdb2ins ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIQO85tj/libz.so.1) best wishes Phil > On 25 Oct 2016, at 20:31, George Sheldrick > wrote: > > SHELXL may be used to refine both small and macromolecular structures against > X-ray or neutron diffraction data, including non-merohedral twins. A new > version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has > been well tested by about 20 volunteers to whom I am very grateful. A new > version of Anna Luebben's program PDB2INS is also available there (for 64 bit > systems only). PDB2INS makes the preparation of the .ins and .hkl files to > run macromolecular SHELXL refinements much easier. For most structures > deposited in the PDB since 2008 these two files can be generated > automatically and no changes are needed to run SHELXL. > > George > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-33021 or -33068 > Fax. +49-551-39-22582 > >
[ccp4bb] New version SHELXL 2016/6 and PDB2INS
SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very grateful. A new version of Anna Luebben's program PDB2INS is also available there (for 64 bit systems only). PDB2INS makes the preparation of the /.ins/ and /.hkl /files to run macromolecular SHELXL refinements much easier. For most structures deposited in the PDB since 2008 these two files can be generated automatically and no changes are needed to run SHELXL. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
