[molpro-user] Molpro 2010.1-23 on CentOS 6.0 does not work
Peter Ruprecht
peter.ruprecht at jila.colorado.edu
Wed Dec 21 20:01:04 GMT 2011
This bug has recently been fixed in RedHat Enterprise 6.2 with package
glibc-2.12-1.47.el6. Presumably this update will make it downstream to
CentOS6 at some point.
-Peter Ruprecht
JILA / University of Colorado
Andy May wrote:
> David,
>
> I have finally found the problem. This appears to be a bug in glibc
> which ships with CentOS6.0. The bug means that some static binaries can
> not be used on the OS.
>
> The bug was also present in Fedora Core 12 and 13:
>
> https://bugzilla.redhat.com/show_bug.cgi?id=597578
>
> where Fedora decided not to patch the bug, but instead waited to Fedora
> Core 14. It appears CentOS is not fast to update packages, and CentOS
> 5.6 contained a version of glibc before the bug was introduced, but
> version 6.0 contains the bug. It seems odd to me that CentOS would ship
> a new release with a version of glibc containing a known bug that has
> been fixed in the parent distribution for some time, but this is the
> situation I'm afraid. There is no solution for the binaries, but your
> source code build will be more optimal in any case.
>
> Best wishes,
>
> Andy
>
> On 08/09/11 13:53, David Danovich wrote:
>> Dear Andy,
>> It does not help. I put it into .cshrc file (setenv TMPDIR /tmp). I put
>> export TMPDIR=/tmp into molpro file. Nothing help.
>> David
>> On Thu, Sep 8, 2011 at 3:40 PM, Andy May <MayAJ1 at cardiff.ac.uk
>> <mailto:MayAJ1 at cardiff.ac.uk>> wrote:
>>
>> David,
>>
>> I think I see the problem, you have not set the value of environment
>> variable TMPDIR. Although Molpro itself will select an appropriate
>> location if the variable is not set, the parallel.x launcher from
>> Global Arrays requires this to be set (Presumably openmpi launcher
>> does not require this, hence why your source code install worked).
>> Please set the variable, eg:
>>
>> export TMPDIR=/tmp
>>
>> and then try.
>>
>> Best wishes,
>>
>> Andy
>>
>>
>> On 08/09/11 13:15, David Danovich wrote:
>>
>> Dear Andy,
>> I have run command molpro -v -n 2 h2-hf.com <http://h2-hf.com>
>> <http://h2-hf.com> >& OUTPUT &
>>
>> Only output file was created in the directory. So I attached
>> this OUTPUT
>> file together with input file (I just changed extension from
>> com to
>> txt-com). I also have compiled molpro-2010.1-23 using source
>> code and it
>> works fine under CentOS6.0 I attached output file OUTPUT-work
>> from this
>> calculation as well (may be it will help you to understand the
>> problem).
>> Thank you David
>> On Thu, Sep 8, 2011 at 1:35 PM, Andy May <MayAJ1 at cardiff.ac.uk
>> <mailto:MayAJ1 at cardiff.ac.uk>
>> <mailto:MayAJ1 at cardiff.ac.uk <mailto:MayAJ1 at cardiff.ac.uk>>>
>> wrote:
>>
>> David,
>>
>> Please could you create a new directory, copy in the input
>> file and
>> then run again with -v option, i.e.:
>>
>> molpro -v -n 4 h2-hf.com <http://h2-hf.com>
>> <http://h2-hf.com>
>>
>>
>> and then send the full output along with any files in the
>> directory,
>> including the input file.
>>
>> Best wishes,
>>
>> Andy
>>
>>
>> On 07/09/11 14:44, David Danovich wrote:
>>
>> Hello,
>> I have installed molpro-mpp-2010.1-23.Linux_____x86_64 on
>> CentOS6.0 (from
>> binary file) and got following error message (command:
>> molpro
>> -n 4
>> h2-hf.com <http://h2-hf.com> <http://h2-hf.com>
>> <http://h2-hf.com> )
>>
>>
>>
>> tmp =
>>
>>
>> /home/dodik/pdir//home/dodik/____PROGRAMS/molpro-2010-1-23/____molprop_2010_1_Linux_x86_64_____i8.exe.p
>>
>> Creating: host=lewis.ch.huji.ac.il
>> <http://lewis.ch.huji.ac.il>
>> <http://lewis.ch.huji.ac.il> <http://lewis.ch.huji.ac.il>,
>>
>>
>> user=dodik,
>>
>>
>>
>> file=/home/dodik/PROGRAMS/____molpro-2010-1-23/molprop_2010_____1_Linux_x86_64_i8.exe,
>>
>> port=45855
>> forrtl: severe (71): integer divide by zero
>> Image PC
>> Routine Line
>> Source
>> Unknown 00002AB8957BDD63 Unknown
>> Unknown Unknown
>> Unknown 00002AB8957ABE3D Unknown
>> Unknown Unknown
>> Unknown 00002AB89553BBA3 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 00000000035EE0DD Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 00000000035EDF16 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 0000000003230629 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 0000000003231044 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 000000000322CE76 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 000000000322DB1B Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 000000000184887B Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 0000000001845B62 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 0000000000402C0F Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 0000000000400535 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 00000000004004DC Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 000000000359EB99 Unknown
>> Unknown Unknown
>> molprop_2010_1_Li 00000000004003A9 Unknown
>> Unknown Unknown
>> 4: interrupt(1)
>>
>> [1] Done molpro -n 4
>> h2-hf.com <http://h2-hf.com>
>> <http://h2-hf.com>
>> <http://h2-hf.com>
>>
>>
>> when I try to run a simple input which works fine on
>> CentOS5.6. The
>> program actually does not start because the same error
>> I got when I
>> used just command
>> molpro &
>> May be somebody already found the solution for this
>> problem.
>> Thank you David
>>
>>
>>
>> ___________________________________________________
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>> <mailto:Molpro-user at molpro.net <mailto:Molpro-user at molpro.net>__>
>>
>> http://www.molpro.net/mailman/____listinfo/molpro-user
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>> <http://www.molpro.net/mailman/listinfo/molpro-user>>
>>
>>
>>
>>
>> --
>> ____________________________________________________________________________
>>
>> Dr. David Danovich, The Lise Meitner Minerva Center for Computational
>> Quantum Chemistry,
>> Institute of Chemistry, The Hebrew University, Edmond J. Safra Campus -
>> Givat Ram,
>> 91904 Jerusalem, Israel http://yfaat.ch.huji.ac.il/david.html,
>> david.danovich at huji.ac.il <mailto:david.danovich at huji.ac.il>
>> FAX:(+972)-2-6584033, Phone:(+972)-2-6586934(w),
>> Mobile:(+972)-544-768669
>>
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