Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS

[Robert Esnouf]

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 <CCP4BB@JISCMAIL.AC.UK> (on behalf of George 
>Sheldrick <gshe...@shelx.uni-ac.gwdg.de>)
>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<p...@mrc-lmb.cam.ac.uk>  
>> 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<gshe...@shelx.uni-ac.gwdg.de>  
>>>> 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

[George Sheldrick]

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

[R.D. Oeffner]

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

[Kay Diederichs]

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

[Tim Gruene]

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

[Anna Luebben]

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

[Martín Martínez Ripoll]

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

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 <gshe...@shelx.uni-ac.gwdg.de>
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

[Phil Evans]

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

[George Sheldrick]

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