From owner-chemistry@ccl.net Thu Feb 10 12:46:00 2011
From: "angela bruneau amb458:cornell.edu" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Gaussian jobs failing with no explanation
Message-Id: <-43927-110210124445-24480-p7TKD6LgLjpi3S91RiBNdA^_^server.ccl.net>
X-Original-From: "angela bruneau" <amb458===cornell.edu>
Date: Thu, 10 Feb 2011 12:44:43 -0500
Sent to CCL by: "angela bruneau" [amb458-$-cornell.edu]
Hi, I'm getting random job failures, no explanation given. Here are some examples:
Job specs:
%mem=10GB
%NProcShared=8
#N MP2/6-311+G(d,p) SP SCF=tight
lda_s2_gs_6311gdp_mp2_2
0,1
[coords]
The last few lines in the out file are:
The electronic state of the initial guess is 1-A.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
Initial convergence to 1.0D-05 achieved. Increase integral accuracy.
SCF Done: E(RHF) = -1056.81565346 A.U. after 14 cycles
Convg = 0.3658D-08 -V/T = 2.0012
ExpMin= 7.40D-03 ExpMax= 8.59D+03 ExpMxC= 1.30D+03 IAcc=3 IRadAn= 5 AccDes=
0.00D+00
HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV=-2
ScaDFX= 1.000000 1.000000 1.000000 1.000000
Range of M.O.s used for correlation: 27 836
NBasis= 836 NAE= 100 NBE= 100 NFC= 26 NFV= 0
NROrb= 810 NOA= 74 NOB= 74 NVA= 736 NVB= 736
**** Warning!!: The largest alpha MO coefficient is 0.11349443D+03
Disk-based method using OVN memory for 74 occupieds at a time.
Estimated scratch disk usage= 46128967232 words.
Actual scratch disk usage= 44910539328 words.
JobTyp=1 Pass 1: I= 1 to 74 NPSUse= 8 ParTrn=T ParDer=T DoDerP=F.
Erroneous write. Write 3457024 instead of 8384512.
fd = 4
orig len = 8384512 left = 8384512
Erroneous write. Write 3457024 instead of 8384512.
fd = 4
orig len = 8384512 left = 8384512
g_write
g_write: Success
-----
Example 2:
Input:
%mem=10GB
%NProcShared=8
#N B3LYP/6-31G(d) FREQ test temperature=213.15
Methylacetatex2_Lix2_gs_180degree_freq_2
0,1
[coordinates]
The last few lines in the out file are:
"o special actions if energy rises.
SCF Done: E(RB3LYP) = -1246.30910382 A.U. after 12 cycles
Convg = 0.9518D-08 -V/T = 2.0097
Range of M.O.s used for correlation: 1 504
NBasis= 504 NAE= 108 NBE= 108 NFC= 0 NFV= 0
NROrb= 504 NOA= 108 NOB= 108 NVA= 396 NVB= 396
**** Warning!!: The largest alpha MO coefficient is 0.18638569D+02
Symmetrizing basis deriv contribution to polar:
IMax=3 JMax=2 DiffMx= 0.00D+00
G2DrvN: will do 71 centers at a time, making 1 passes doing MaxLOS=2.
Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00.
FoFDir/FoFCou used for L=0 through L=2.
End of G2Drv Frequency-dependent properties file 721 does not exist.
End of G2Drv Frequency-dependent properties file 722 does not exist.
IDoAtm=11111111111111111111111111111111111111111111111111
IDoAtm=11111111111111111111
Differentiating once with respect to electric field.
with respect to dipole field.
Differentiating once with respect to nuclear coordinates.
There are 213 degrees of freedom in the 1st order CPHF. IDoFFX=5.
213 vectors produced by pass 0 Test12= 4.28D-14 1.00D-09 XBig12= 1.82D+02 4.35D+00.
AX will form 72 AO Fock derivatives at one time.
212 vectors produced by pass 1 Test12= 4.28D-14 1.00D-09 XBig12= 2.01D+01 9.09D-01.
210 vectors produced by pass 2 Test12= 4.28D-14 1.00D-09 XBig12= 1.72D-01 2.53D-02.
210 vectors produced by pass 3 Test12= 4.28D-14 1.00D-09 XBig12= 3.78D-04 2.18D-03.
210 vectors produced by pass 4 Test12= 4.28D-14 1.00D-09 XBig12= 4.01D-07 5.18D-05.
95 vectors produced by pass 5 Test12= 4.28D-14 1.00D-09 XBig12= 2.85D-10 1.20D-06.
6 vectors produced by pass 6 Test12= 4.28D-14 1.00D-09 XBig12= 2.04D-13 4.54D-08."
Both of these jobs failed at this point. I have many other jobs failing as well. Not sure what the deal
is, never had these problems before. Sometimes when restarted they work, sometimes not. Any
thoughts?
Thanks for any insight.
From owner-chemistry@ccl.net Thu Feb 10 14:14:00 2011
From: "William F. Polik polik]|[hope.edu" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: WebMO user interface: Possible to read checkfiles?
Message-Id: <-43928-110210114427-4107-eJX8e3k/uaMacvxBZLCB/g..server.ccl.net>
X-Original-From: "William F. Polik" <polik]*[hope.edu>
Content-Type: multipart/alternative;
boundary="------------050200040306040209090505"
Date: Thu, 10 Feb 2011 11:44:12 -0500
MIME-Version: 1.0
Sent to CCL by: "William F. Polik" [polik*hope.edu]
This is a multi-part message in MIME format.
--------------050200040306040209090505
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
Angela,
Thank you for reporting this. We have verified that WebMO 10.1 and some
earlier versions contain a bug whereby Gaussian checkpoint files which
are saved cannot be properly reused in a future calculation via the "Use
Checkpoint File" option under "Advanced Job Options". This issue will be
fixed in the next release.
In the meantime, we have released a patch file that will also fix the
issue, which can be downloaded from our Support Forum at
http://www.webmo.net/discus/support/messages/5/434.html
(The patch is just a 3 line addition, so you could also easily manually
edit the gaussian.cgi file.)
Will Polik
On 2/8/11 7:43 AM, Thomas Patko tpatko*gmail.com wrote:
> Dear Angela:
>
> Did you already contact WebMO about this issue? JR is really rather
> good about support for these sort of questions. You can post here:
>
> http://www.webmo.net/forum.html
>
> Cheers,
>
> Thomas
>
> On Mon, Feb 7, 2011 at 8:13 AM, angela bruneau amb458..cornell.edu
> <http://cornell.edu> <owner-chemistry[#]ccl.net
> <mailto:owner-chemistry[#]ccl.net>> wrote:
>
>
> Sent to CCL by: "angela bruneau" [amb458##cornell.edu
> <http://cornell.edu>]
> I have had no success in getting check files read in with WebMO
> submitting Gaussian calcs. It seems there is a file problem. WebMO
> seems to create the file that it works in at the time you hit
> submit; it assigns a directory/job name, and all reads and writes
> must come from there. You cannot read from other directories
> (perhaps a Fortran problem) and you cannot specify a directory in
> lieu of WebMO choosing one.
>
> If I am wrong, and there is a way, please let me know. Otherwise I
> guess people are generally building in GV or Avogadro or
> something, then just running jobs through command line? I might
> have to go this route. The thing I like about WebMO is that I can
> see the energy graph as the job is running so I know quickly if it
> is oscillating, or if it is generally dropping. What does everyone
> else do who is not using WebMO?
>
> Thanks!!
> Angela
>
>
--
------------------------------------------------------------------------
Dr. William F. Polik
Hofma Professor of Chemistry
Department of Chemistry
Hope College
35 East 12th Street
Holland, MI 49422-9000
USA
polik^hope.edu
http://www.chem.hope.edu/~polik <http://www.chem.hope.edu/%7Epolik>
tel: (616) 395-7639
fax: (616) 395-7118
------------------------------------------------------------------------
--------------050200040306040209090505
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Angela,<br>
<br>
Thank you for reporting this. We have verified that WebMO 10.1 and
some earlier versions contain a bug whereby Gaussian checkpoint
files which are saved cannot be properly reused in a future
calculation via the "Use Checkpoint File" option under "Advanced Job
Options". This issue will be fixed in the next release.<br>
<br>
In the meantime, we have released a patch file that will also fix
the issue, which can be downloaded from our Support Forum at<br>
<a class="moz-txt-link-freetext" href="http://www.webmo.net/discus/support/messages/5/434.html">http://www.webmo.net/discus/support/messages/5/434.html</a><br>
<br>
(The patch is just a 3 line addition, so you could also easily
manually edit the gaussian.cgi file.)<br>
<br>
Will Polik<br>
<br>
On 2/8/11 7:43 AM, Thomas Patko tpatko*gmail.com wrote:
<blockquote
cite="mid:-id%233dr-43906-110208074347-15794-WHMdOwdiAMMuaDJQp+4Mzg^server.ccl.net"
type="cite">Dear Angela:<br>
<br>
Did you already contact WebMO about this issue? JR is really
rather good about support for these sort of questions. You can
post here:<br>
<br>
<a moz-do-not-send="true" href="http://www.webmo.net/forum.html">http://www.webmo.net/forum.html</a><br>
<br>
Cheers,<br>
<br>
Thomas<br>
<br>
<div class="gmail_quote">On Mon, Feb 7, 2011 at 8:13 AM, angela
bruneau amb458..<a moz-do-not-send="true"
href="http://cornell.edu">cornell.edu</a> <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:owner-chemistry[#]ccl.net">owner-chemistry[#]ccl.net</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;"><br>
Sent to CCL by: "angela bruneau" [amb458##<a
moz-do-not-send="true" href="http://cornell.edu"
target="_blank">cornell.edu</a>]<br>
I have had no success in getting check files read in with
WebMO submitting Gaussian calcs. It seems there is a file
problem. WebMO seems to create the file that it works in at
the time you hit submit; it assigns a directory/job name, and
all reads and writes must come from there. You cannot read
from other directories (perhaps a Fortran problem) and you
cannot specify a directory in lieu of WebMO choosing one.<br>
<br>
If I am wrong, and there is a way, please let me know.
Otherwise I guess people are generally building in GV or
Avogadro or something, then just running jobs through command
line? I might have to go this route. The thing I like about
WebMO is that I can see the energy graph as the job is running
so I know quickly if it is oscillating, or if it is generally
dropping. What does everyone else do who is not using WebMO?<br>
<br>
Thanks!!<br>
Angela<br>
<br>
<br>
</blockquote>
</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<title></title>
<hr size="2" width="100%">Dr. William F. Polik<br>
Hofma Professor of Chemistry<br>
<br>
Department of Chemistry<br>
Hope College<br>
35 East 12th Street<br>
Holland, MI 49422-9000<br>
USA<br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:polik^hope.edu">polik^hope.edu</a><br>
<a href="http://www.chem.hope.edu/%7Epolik">http://www.chem.hope.edu/~polik</a><br>
tel: (616) 395-7639<br>
fax: (616) 395-7118<br>
<hr size="2" width="100%">
</div>
</body>
</html>
--------------050200040306040209090505--
From owner-chemistry@ccl.net Thu Feb 10 14:49:00 2011
From: "Artem Masunov amasunov : gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: Gaussian jobs failing with no explanation
Message-Id: <-43929-110210134226-32122-nyLsWK86zf6yHin+yjOKHQ%%server.ccl.net>
X-Original-From: Artem Masunov <amasunov##gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 10 Feb 2011 13:42:18 -0500
MIME-Version: 1.0
Sent to CCL by: Artem Masunov [amasunov()gmail.com]
This simply means HD is out of space for output or scratch files
On Thu, Feb 10, 2011 at 12:44 PM, angela bruneau amb458:cornell.edu
<owner-chemistry(~)ccl.net> wrote:
>
> Sent to CCL by: "angela �bruneau" [amb458-$-cornell.edu]
> Hi, I'm getting random job failures, no explanation given. Here are some examples:
>
> Job specs:
> �%mem=10GB
> �%NProcShared=8
> �#N MP2/6-311+G(d,p) SP SCF=tight
>
> �lda_s2_gs_6311gdp_mp2_2
>
> 0,1
> [coords]
>
> The last few lines in the out file are:
> �The electronic state of the initial guess is 1-A.
> �Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
> �Requested convergence on MAX density matrix=1.00D-06.
> �Requested convergence on � � � � � � energy=1.00D-06.
> �No special actions if energy rises.
> �Initial convergence to 1.0D-05 achieved. �Increase integral accuracy.
> �SCF Done: �E(RHF) = �-1056.81565346 � � A.U. after � 14 cycles
> � � � � � � Convg �= � �0.3658D-08 � � � � � � -V/T = �2.0012
> �ExpMin= 7.40D-03 ExpMax= 8.59D+03 ExpMxC= 1.30D+03 IAcc=3 IRadAn= � � � � 5 AccDes=
> 0.00D+00
> �HarFok: �IExCor= �205 AccDes= 0.00D+00 IRadAn= � � � � 5 IDoV=-2
> �ScaDFX= �1.000000 �1.000000 �1.000000 �1.000000
> �Range of M.O.s used for correlation: � �27 � 836
> �NBasis= � 836 NAE= � 100 NBE= � 100 NFC= � �26 NFV= � � 0
> �NROrb= � �810 NOA= � �74 NOB= � �74 NVA= � 736 NVB= � 736
>
> �**** Warning!!: The largest alpha MO coefficient is �0.11349443D+03
>
> �Disk-based method using OVN memory for 74 occupieds at a time.
> �Estimated scratch disk usage= 46128967232 words.
> �Actual � �scratch disk usage= 44910539328 words.
> �JobTyp=1 Pass �1: �I= � 1 to �74 NPSUse= �8 ParTrn=T ParDer=T DoDerP=F.
> Erroneous write. Write 3457024 instead of 8384512.
> fd = 4
> orig len = 8384512 left = 8384512
> Erroneous write. Write 3457024 instead of 8384512.
> fd = 4
> orig len = 8384512 left = 8384512
> g_write
> g_write: Success
>
> -----
>
> Example 2:
>
> Input:
> %mem=10GB
> %NProcShared=8
> #N B3LYP/6-31G(d) FREQ test temperature=213.15
>
> Methylacetatex2_Lix2_gs_180degree_freq_2
>
> 0,1
> [coordinates]
>
> The last few lines in the out file are:
>
> "o special actions if energy rises.
> �SCF Done: �E(RB3LYP) = �-1246.30910382 � � A.U. after � 12 cycles
> � � � � � � Convg �= � �0.9518D-08 � � � � � � -V/T = �2.0097
> �Range of M.O.s used for correlation: � � 1 � 504
> �NBasis= � 504 NAE= � 108 NBE= � 108 NFC= � � 0 NFV= � � 0
> �NROrb= � �504 NOA= � 108 NOB= � 108 NVA= � 396 NVB= � 396
>
> �**** Warning!!: The largest alpha MO coefficient is �0.18638569D+02
>
> �Symmetrizing basis deriv contribution to polar:
> �IMax=3 JMax=2 DiffMx= 0.00D+00
> �G2DrvN: will do � �71 centers at a time, making � �1 passes doing MaxLOS=2.
> �Calling FoFCou, ICntrl= �3107 FMM=T I1Cent= � 0 AccDes= 0.00D+00.
> �FoFDir/FoFCou used for L=0 through L=2.
> �End of G2Drv Frequency-dependent properties file � 721 does not exist.
> �End of G2Drv Frequency-dependent properties file � 722 does not exist.
> � � � � �IDoAtm=11111111111111111111111111111111111111111111111111
> � � � � �IDoAtm=11111111111111111111
> � � � � �Differentiating once with respect to electric field.
> � � � � � � � �with respect to dipole field.
> � � � � �Differentiating once with respect to nuclear coordinates.
> � � � � �There are � 213 degrees of freedom in the 1st order CPHF. �IDoFFX=5.
> � �213 vectors produced by pass �0 Test12= 4.28D-14 1.00D-09 XBig12= 1.82D+02 4.35D+00.
> �AX will form � �72 AO Fock derivatives at one time.
> � �212 vectors produced by pass �1 Test12= 4.28D-14 1.00D-09 XBig12= 2.01D+01 9.09D-01.
> � �210 vectors produced by pass �2 Test12= 4.28D-14 1.00D-09 XBig12= 1.72D-01 2.53D-02.
> � �210 vectors produced by pass �3 Test12= 4.28D-14 1.00D-09 XBig12= 3.78D-04 2.18D-03.
> � �210 vectors produced by pass �4 Test12= 4.28D-14 1.00D-09 XBig12= 4.01D-07 5.18D-05.
> � � 95 vectors produced by pass �5 Test12= 4.28D-14 1.00D-09 XBig12= 2.85D-10 1.20D-06.
> � � �6 vectors produced by pass �6 Test12= 4.28D-14 1.00D-09 XBig12= 2.04D-13 4.54D-08."
>
> Both of these jobs failed at this point. I have many other jobs failing as well. Not sure what the deal
> is, never had these problems before. Sometimes when restarted they work, sometimes not. Any
> thoughts?
>
> Thanks for any insight.> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message> � � �http://www.ccl.net/chemistry/sub_unsub.shtml> � � �http://www.ccl.net/spammers.txt>
>
>
From owner-chemistry@ccl.net Thu Feb 10 18:07:00 2011
From: "rocky walden rocky.walden19 _ gmail.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Explanation / Guidance needed..
Message-Id: <-43930-110210173512-18284-DyARyF9wu2A/rYqfyJCU/A%x%server.ccl.net>
X-Original-From: rocky walden <rocky.walden19^gmail.com>
Content-Type: multipart/alternative; boundary=00c09fa9c4ff36db71049bf53159
Date: Thu, 10 Feb 2011 23:35:01 +0100
MIME-Version: 1.0
Sent to CCL by: rocky walden [rocky.walden19||gmail.com]
--00c09fa9c4ff36db71049bf53159
Content-Type: text/plain; charset=ISO-8859-1
Hello All,
I am new to this Computational chemistry, i am planning to do some
Pratical course in Computational Chemisty focusing some MD Simulations of a
Protein with a set of synthesized ligands.
We have NAMD, GROMACS Suite for Calculations / simulations and have a
cluster with 40 processors (Dual core).
I am struck with which type of simulation should i do Either Picosecond
or FemtoSecond or Nanosecond simulation.
What are the different types of simulations available based on time
scale (pico/femto/nano/ Micro).
What should be the size of steps ( what happens when i use more no of
steps / or i decrease the no of steps).
Thanks
walden.R
--00c09fa9c4ff36db71049bf53159
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Hello All,<br>=A0=A0=A0=A0=A0=A0 <br>=A0=A0=A0=A0=A0 I am new to this Compu=
tational chemistry, i am planning to do some Pratical course in Computation=
al Chemisty focusing some MD Simulations of a Protein with a set of synthes=
ized ligands.<br>=A0=A0=A0=A0=A0 We have NAMD, GROMACS=A0 Suite for Calcula=
tions / simulations and have a cluster with 40 processors (Dual core).<br>
=A0=A0=A0=A0=A0 <br>=A0=A0=A0=A0 I am struck with which type of simulation =
should i do Either Picosecond or FemtoSecond=A0 or Nanosecond simulation.<b=
r>=A0=A0=A0=A0 What are the different types of simulations available based =
on time scale (pico/femto/nano/ Micro).<br>
=A0=A0=A0 What should be the size of steps ( what happens when i use more n=
o of steps / or i decrease the no of steps).<br>=A0=A0 <br><br><br>Thanks<b=
r>walden.R<br>=A0=A0=A0=A0=A0 <br>
--00c09fa9c4ff36db71049bf53159--
From owner-chemistry@ccl.net Thu Feb 10 21:23:00 2011
From: "Michael Banck michael.banck#%#ch.tum.de" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: Reference configurations for 2-state MRCI calculations in MOLPRO
Message-Id: <-43931-110210172726-27190-sKFt/Hgs6iQYNm6ZnvScbw:+:server.ccl.net>
X-Original-From: Michael Banck <michael.banck.:+:.ch.tum.de>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Thu, 10 Feb 2011 23:26:49 +0100
MIME-Version: 1.0
Sent to CCL by: Michael Banck [michael.banck:+:ch.tum.de]
On Tue, Feb 08, 2011 at 09:13:33AM -0500, Marcin Andrzejak andrzeja()chemia.uj.edu.pl wrote:
> Sent to CCL by: "Marcin Andrzejak" [andrzeja#,#chemia.uj.edu.pl]
> I am a new user of MOLPRO, and I am having problems with selecting
> reference configurations from preceding two-states state-average
> CASSCF calculations for the MRCI treatment.
>
> My input looks like that:
>
> {multi
> closed,18,1,17,1
> occ,18,6,17,6
> wf,86,3,0;state,2
> accuracy,gradient=1.0D-6,step=1.0e-5,econv=1.0d-9
> maxiter,15
> }
>
> {ci
> closed,18,1,17,1
> occ,18,6,17,6
> core,8,1,8,1
> wf,86,3,0;state,2,1,2
> select
> con,2,2,2,1,0,2,2,1,0,0
> con,2,2,2,1,0,2,1,2,0,0
> con,2,2,2,0,1,2,2,1,0,0
> con,2,2,2,1,0,2,2,0,1,0
> }
>
> This input works perfectly as long as I require only the lowest CI
> root - MRCI reports selected configurations and calculations go on
> smoothly.
The above input selects both roots, so did you remove the state card in
the lowest CI root case?
> However, when I specify two CI roots to be optimized in
> MRCI, then it takes all the configurations from CASSCF and crashes
> down due to the obvious memory problem.
I believe the problem is that the ci program in Molpro stops parsing the
wavefunction-specific input when it encounters the state card. I.e., the
select and subsequent con cards are ignored. This is different to how the
multi program handles selecting configurations and states.
Put the state card after the select/con cards.
Best regards,
Michael
From owner-chemistry@ccl.net Thu Feb 10 21:58:00 2011
From: "Sidney Ramos Santana santanasidney()yahoo.com.br" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: SOLVED Molpro execution problem in Ubuntu 10
Message-Id: <-43932-110210170809-18532-XGX7CyeWdLPlWMg3nieQsA++server.ccl.net>
X-Original-From: "Sidney Ramos Santana" <santanasidney###yahoo.com.br>
Date: Thu, 10 Feb 2011 17:08:07 -0500
Sent to CCL by: "Sidney Ramos Santana" [santanasidney#%#yahoo.com.br]
Dear CCL Users,
I am very grateful for the answers
that has been sending to me.
I think the Molpro 2009 has been running well
until the Ubuntu 9.10.
So, I solved my Molpro problem when I upgrade it to
the lastest Molpro 2010 binay version.
Now it is running well in Ubuntu 10.04 64 bits.
Thanks you so much to everyone.
Best Regards,
Sidney R. Santana
e-mail:santanasidney_at_yahoo.com.br
=================================================
The question can be read bellow:
=================================================
Dear CCL & Molpro Users,
Please could anyone help me?
I am trying to execute the Molpro 2009 in a computer with
Ubuntu 10.04 64 bits (Kernel Version: 2.6.32-28 SMP, and
libc6 Version: 2.11.1-0ubuntu7.8).
But the program have been stopped
and typed the following error:
/opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, len=50
cf3cl_8.inp, len=11
-master, len=7
ubuntu, len=6
39720, len=5
1, len=1
1, len=1
0, len=1
0, len=1
molprop_2009_1_Linux_x86_64_i8.exe: relocation error: /lib/libnss_files.so.2:
symbol __r awmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with
link time reference
tmp = /home/sidney/pdir//opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe.p
Creating: host=ubuntu, user=elizete,
file=/opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, port=39720
1: interrupt(1)
Is this a Ubuntu version problem ?
Please could anyone tell me what is wrong and how can I fix that ?
Thanks for any help.
Best Regards,
Sidney R. Santana
e-mail:santanasidney_at_yahoo.com.br
=================================================
The answers can be read bellow:
=================================================
> From:
"Pietro Ottati pietro.ottati:-:gmail.com" <owner-chemistry_at_ccl.net>
To:
"Santana, Sidney Ramos " <santanasidney_at_yahoo.com.br>
I'm not an expert but do you set export LD_LIBRARY_PATH in your /etc/profile to
define where is the library?
check MANUAL or INSTALL or REAME file of molpro...
I don't use it but it's possible that the solution...
---------------------
> From:
"Kirk Peterson kipeters_._wsu.edu" <owner-chemistry_at_ccl.net>
To:
"Santana, Sidney Ramos " <santanasidney_at_yahoo.com.br>
Sent to CCL by: Kirk Peterson [kipeters .. wsu.edu]
Dear Sidney,
looks like an installation problem. Do the test jobs work? Which compiler are you using?
I would strongly recommend to post this to the Molpro users list (molpro-user at molpro.net). You'll
certainly get this worked out there.
regards,
-Kirk
---------------------
> From:
"James Womack james.c.womack_._gmail.com" <owner-chemistry_at_ccl.net>
To:
"Santana, Sidney Ramos " <santanasidney_at_yahoo.com.br>
Sent to CCL by: James Womack [james.c.womack||gmail.com]
I can't offer any suggestions on how to fix the problem but I can tell
you that it's not a problem with Ubuntu generally. I'm running version
2010.1 (compiled from source) without problem on Ubuntu 10.04 32 bit. As
someone else said, it's worth going to the Molpro developers/mailing
list directly with this problem.
Hope you fix it soon,
James
---------------------
> From:
"Andy May" <MayAJ1_at_cardiff.ac.uk>
To:
"Sidney Santana" <santanasidney_at_yahoo.com.br>
Cc:
molpro-user_at_molpro.net
Sidney,
Can you first try with the latest Molpro binaries (2010)? These are
built on a more recent OS and with the latest version of the compilers.
Best wishes,
Andy
---------------------
> From:
"Thomas Ritschel" <ritschel_at_uni-potsdam.de>
To:
molpro-user_at_molpro.net, santanasidney_at_yahoo.com.br, MayAJ1_at_cardiff.ac.uk
Dear Sidney and Andy,
in the latest Ubuntus (10.04 and 10.10) the glibc library was replaced by the
so called "embedded glibc" (eglibc). It seems that this is not 100%
compatible to the standard glibc, at least if the binaries are generated on a
system which uses the standard glibc (leading to "undefined symbol" errors as
in your output).
> From my own tests I found that both 2009 and 2010 are not working on Ubuntu
10.04 and 10.10. The only option is to compile it from source.
Kind regards,
Thomas Ritschel
---------------------
Institut fuer Chemie
Universitaet Potsdam
Germany
---------------------
> From:
"Konstantin Tokarev" <annulen_at_yandex.ru>
To:
"Thomas Ritschel" <ritschel_at_uni-potsdam.de>
Cc:
molpro-user_at_molpro.net, santanasidney_at_yahoo.com.br, mayaj1_at_cardiff.ac.uk
10.02.2011, 15:15, "Thomas Ritschel" <ritschel_at_uni-potsdam.de>:
> Dear Sidney and Andy,
>
> in the latest Ubuntus (10.04 and 10.10) the glibc library was replaced by the
> so called "embedded glibc" (eglibc). It seems that this is not 100%
> compatible to the standard glibc, at least if the binaries are generated on a
> system which uses the standard glibc (leading to "undefined symbol" errors as
> in your output).
>
> From my own tests I found that both 2009 and 2010 are not working on Ubuntu
> 10.04 and 10.10. The only option is to compile it from source.
AFAIK, eglibc team claims that they keep binary compatibility with glibc
--
Regards,
Konstantin
-------------------------------------------
From owner-chemistry@ccl.net Thu Feb 10 22:33:00 2011
From: "Michael Banck michael.banck],[ch.tum.de" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: WebMO user interface: Possible to read checkfiles?
Message-Id: <-43933-110210170257-6662-H1vothDqOzZrBNL3Ismp1A . server.ccl.net>
X-Original-From: Michael Banck <michael.banck]|[ch.tum.de>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Thu, 10 Feb 2011 23:02:42 +0100
MIME-Version: 1.0
Sent to CCL by: Michael Banck [michael.banck+*+ch.tum.de]
On Tue, Feb 08, 2011 at 01:33:30AM -0500, Patrick Mccarren patrick.mccarren#%#gmail.com wrote:
> Molden is a great visualizer to keep track of a job. You get the
> energy graphs and visualization of the molecule at each step. The
> graphics aren't fancy but it is extremely fast and great for slow X11
> connections.
As far as I know, this visualization is after the fact though, isn't it?
I.e., you can step through a finished compute job and view each step,
but you cannot monitor a computation as it runs, right?
Michael