Re: [ccp4bb] ccp4i problem - bad marshal data

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Rapid Access slot available at LS-CAT at the APS
From: Joe Brunzelle joeb {- at -} LS-CAT {- dot -} ORG
Date: 2009-06-04

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Subject: CCP4i problem on RHEL5
From: Mary Fitzgerald mary {- dot -} x {- dot -} fitzgerald {- at -} GMAIL {- dot -} COM
Date: 2009-06-04

Subject: Re: ccp4i problem - bad marshal data
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2009-06-04

Hi Charles and all,
thanks a lot. That did the trick for ccp4i.

There still are some marshal-related issues around.

a) ccp4i
after each job I get a message like this:
CreateAnnotatedLogfile: failed for /..xxxx..../7_refmac5.log: Traceback
(most recent call last):
File "/usr/local/ccp4-6.1.1/ccp4-6.1.1/share/smartie/baubles.py", line 18,
in ?
import smartie
ValueError: bad marshal data

b) xia2:
[user@sbl-emerald xia]# xia2 ../images/203289a7_a0001.img
Traceback (most recent call last):
File "/usr/local/xia2/xia2-0.3.0.0/xia2-0.3.0.0//Applications/xia2.py",
line 27, in ?
from Handlers.Streams import Chatter
ValueError: bad marshal data

*ccp4* provides /usr/local/ccp4-6.1.1/Python-2.4.5/bin/python
*centos5.3* runs python-2.4.3-24

Any ideas what happens there?

Cheers
Jan

On Wed, Jun 3, 2009 at 3:31 AM, Ballard, CC (Charles) <
charles.ballard@stfc.ac.uk> wrote:

> Hi Jan
>
> can you delete all .pyc files from $CCP4/share/dbccp4i and try to launch
> again.
>
> marshal is concerned with python object serialization, in particular pyc
> files, which may not be compatible across versions. What version of python
> is the machine using, and has it been updated recently.
>
> Charles Ballard
> CCP4
>
> ------------------------------
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Jan
> Abendroth
> *Sent:* 02 June 2009 22:56
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] ccp4i problem - bad marshal data
>
> Hi all,
> we a one weird problem with one of our machines.
> Upon launching ccp4i, we get an error message in the shell window:
>
> [user1@pahto ~]$ ccp4i
> bad marshal data
>
> Then, once the interface finally starts after quite a while a new window
> opens with the following message. None of the previous projects are visible
> any more.
>
> CCP4i is currently configured to use the database server "dbccp4i" to
> access the job database, but has failed to either start or connect to the
> server this time.
>
> You can continue to use CCP4i and the interface should still operate
> normally, although some advanced functions may not be available.
>
> Next time you start CCP4i it will try again to use the database server. If
> you wish to disable this behaviour then select the option to automatically
> disable use of the server in future sessions.
>
> Any ideas how to get out of this?
>
> Thanks
> Jan
>
> --
> --
> Jan Abendroth
> deCODE biostructures
> Seattle / Bainbridge Island, WA, USA
> work: JAbendroth_at_decode.com
> home: Jan.Abendroth_at_gmail.com
>
> ------------------------------
>
> Scanned by iCritical.
>

--
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island, WA, USA
work: JAbendroth_at_decode.com
home: Jan.Abendroth_at_gmail.com

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Rapid Access slot available at LS-CAT at the APS
From: Joe Brunzelle joeb {- at -} LS-CAT {- dot -} ORG
Date: 2009-06-04

Next message:
Subject: CCP4i problem on RHEL5
From: Mary Fitzgerald mary {- dot -} x {- dot -} fitzgerald {- at -} GMAIL {- dot -} COM
Date: 2009-06-04