From owner-chemistry:~at~:ccl.net Wed May 25 12:14:01 2016 From: "Igors Mihailovs igors.mihailovs0*_*gmail.com" To: CCL Subject: CCL:G: About checkpoint problems after using GaussView 5.0 Message-Id: <-52221-160525121112-9668-SmfhNwi/Ma9GmfntPqeQhg(a)server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=94eb2c086cd6d6b7240533acebcc Date: Wed, 25 May 2016 19:10:48 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0:_:gmail.com] --94eb2c086cd6d6b7240533acebcc Content-Type: text/plain; charset=UTF-8 Dear Daniel, Checkpoint files are indeed usable only on the computer you have generated it, or on some identical node. However, usually I managed, for example, to read geometry for use in restarted or next job on other type node. However, formchk can be done only on the same node as the calculation during which .CHK was produced. Maybe GaussView tries to launch formcheck on your "control node" instead... With best wishes, Igors Mihailovs (engineer / PhD student) Institute of Solid State Physics University of Latvia 2016-05-23 22:05 GMT+03:00 Daniel Morales Salazar danielmoralessalazar91(!) gmail.com : > > Sent to CCL by: "Daniel Morales Salazar" [danielmoralessalazar91: > gmail.com] > Hello, > > Typically I send my jobs using Gaussian 09 by creating text scripts in > the batch mode using UNIX's vi editor. Lately, SLURM gives my jobs > extremely low priorities. I then decided to try the interactive mode, > which allows me to use computational time for shorter times. I do not > know how to use scripts in the interactive mode so I decided to use > Gaussview 5.0.8 to send my jobs. Whenever I want to restart those jobs > (given that the interactive session closes), the checkpoint files are > corrupted in like 99% of the cases. I get the following message: > > "$ module load gaussian/g09.d01 > $ module load gaussian/gv-5.0.8 > $ formchk file.chk file.fchk > Read checkpoint file file.chk > Write formatted file file.fchk > Missing data for FChkPn. > Error termination via Lnk1e at Mon May 23 20:32:58 2016. > Segmentation fault (core dumped)" > > In the few cases that formchk works, when I try to visualize the > checkpoint file in Gaussview, a message like this one appears: > > "CConnectionGFCHK::Parse_GFCH() Missing or bad data: Alpha Orbital > Energies Line Number 574" > > The checkpoint files get corrupted even when re-sending the jobs using > the interactive mode. I have tried reading into the issue but I can't > find any input online. Does this have to do with the fact that the check > point file is only usable in the specific cores I was assigned when > starting the job? can anybody help me solving this issue please? > > Thanks. > > Sincerely, > > Daniel> > > --94eb2c086cd6d6b7240533acebcc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Daniel,

Checkpoint files are indeed= usable only on the computer you have generated it, or on some identical no= de. However, usually I managed, for example, to read geometry for use in re= started or next job on other type node. However, formchk can be done only o= n the same node as the calculation during which .CHK was produced. Maybe Ga= ussView tries to launch formcheck on your "control node" instead.= ..

Wi= th best wishes,
Igors Mihailovs (engineer / PhD student)
<= div>Institute of Solid State Physics
University of Latvia
=


2016-05-23 22:05 GMT+03:00 Daniel Morales Sa= lazar danielmoralessalazar91(!)gmail.com <= span dir=3D"ltr"><owner-chemistry..ccl.net>:

Sent to CCL by: "Daniel=C2=A0 Morales Salazar" [danielmoralessala= zar91:gma= il.com]
Hello,

Typically I send my=C2=A0 jobs using Gaussian 09 by creating text scripts i= n
the batch mode using UNIX's vi editor. Lately, SLURM gives my jobs
extremely low priorities. I then decided to try the interactive mode,
which allows me to use computational time for shorter times. I do not
know how to use scripts in the interactive mode so I decided to use
Gaussview 5.0.8 to send my jobs. Whenever I want to restart those jobs
(given that the interactive session closes), the checkpoint files are
corrupted in like 99% of the cases. I get the following message:

"$ module load gaussian/g09.d01
$ module load gaussian/gv-5.0.8
$ formchk file.chk file.fchk
=C2=A0Read checkpoint file file.chk
=C2=A0Write formatted file file.fchk
=C2=A0Missing data for FChkPn.
=C2=A0Error termination via Lnk1e at Mon May 23 20:32:58 2016.
Segmentation fault (core dumped)"

In the few cases that formchk works, when I try to visualize the
checkpoint file in Gaussview, a message like this one appears:

"CConnectionGFCHK::Parse_GFCH() Missing or bad data: Alpha Orbital
Energies Line Number 574"

The checkpoint files get corrupted even when re-sending the jobs using
the interactive mode. I have tried reading into the issue but I can't find any input online. Does this have to do with the fact that the check point file is only usable in the specific cores I was assigned when
starting the job? can anybody help me solving this issue please?

Thanks.

Sincerely,

Daniel



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY..ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST..ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/



--94eb2c086cd6d6b7240533acebcc--