Hi Naren,
we installed NONMEM V6 at 3 identic Suse Linux Server without problems.
In the Suse Linux Distribution is an gfortran compiler included and this is
in case of NONMEM
a little bit tricky. We created a symbolic link between the gfortran
directory and g77.
After the installation from gfotran, R, NONMEM, PsN and XPOSE at every
Linux server we installed
the SGE with one head and 2 "childs" servers.
Do you need further information please contact me.
Best Regards
Claus
CI Pharmaceuticals - R&D Solutions Management
D41/221
HPC: D041/001
Phone: +49(0)6151 724526
Fax: +49(0)6151 914526
Email: Claus.Neumayer
Merck KGaA
Frankfurter Str. 250
D 64293 Darmstadt
Home: www.merck.de
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Antwort: Install NONMEM on Linux cluster
Hi Naren,
we installed NONMEM V6 at 3 identic Suse Linux Server without problems.
In the Suse Linux Distribution is an gfortran compiler included and this is
in case of NONMEM
a little bit tricky. We created a symbolic link between the gfortran
directory and g77.
After the installation from gfotran, R, NONMEM, PsN and XPOSE at every
Linux server we installed
the SGE with one head and 2 "childs" servers.
Do you need further information please contact me.
Best Regards
Claus
CI Pharmaceuticals - R&D Solutions Management
D41/221
HPC: D041/001
Phone: +49(0)6151 724526
Fax: +49(0)6151 914526
Email: [email protected]
Merck KGaA
Frankfurter Str. 250
D 64293 Darmstadt
Home: www.merck.de
Pflichtangaben finden Sie unter http://mandatories.merck.de
Mandatory Information can be found at http://mandatories.merck.de
This message and any attachment are confidential and may be privileged or
otherwise protected from disclosure. If you are not the intended recipient,
you must not copy this message or attachment or disclose the contents to
any other person. If you have received this transmission in error, please
notify the sender immediately and delete the message and any attachment
from your system. Merck KGaA, Darmstadt, Germany and any of its
subsidiaries do not accept liability for any omissions or errors in this
message which may arise as a result of E-Mail-transmission or for damages
resulting from any unauthorized changes of the content of this message and
any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
subsidiaries do not guarantee that this message is free of viruses and does
not accept liability for any damages caused by any virus transmitted
therewith.
Click http://disclaimer.merck.de to access the German, French, Spanish and
Portuguese versions of this disclaimer.
Hi Naren,
ad 1: Will look them up later on. IIRC nothing special was needed for
g77 in nmqual. The largest chance was needed in PsN, actually. There
some code was added to use the nmqual's 'OUTPUT' filename rather than
the redirection that is configured by nonmem's SETUP
ad 2: We have not tried gfortran (yet)
ad 3: Nothing special was needed next to the standard configuration of
our cluster machines. SGE does not require special libraries, all
operations are performed on OS-level. Except checkpointing (and perhaps
other advanced options), but we never tried that.
ad 4: There is one back-up headnode.
ad 5: One script takes a commandline and submits it to the cluster with
preconfigured options, including e-mail notification. I also have
scripts that do clean-up of psn folders, help with updating of
run-numbers in control streams, automatically draw parameter draws from
the covariance matrix and one that does more detailed diagnostics on the
covariance matrix.
You are welcome!
Best regards,
Jeroen
Jeroen Elassaiss-Schaap, PhD
Modeling & Simulation Expert
Pharmacokinetics, Pharmacodynamics & Pharmacometrics (P3)
Early Clinical Research and Experimental Medicine
Schering-Plough Research Institute
T: +31 41266 9320
PS: I only realized later on that these mails never made it to the list,
excuse me for that.
Quoted reply history
________________________________
From: Narayanan, Naren [mailto:anarayan
Sent: Friday, 02 October, 2009 3:20
To: Elassaiss - Schaap, J. (Jeroen)
Subject: RE: Antwort: [NMusers] Install NONMEM on Linux cluster
Hi Jeroen,
Thanks for your response.
1) Would you be able to share the g77 related changes made in NMQual's
xml files for successful installation with PsN and SGE? We installed NM6
using NMQual (without SGE and PsN). By the way, thanks for reminding
about trapping floating point errors! I would use that option too.
2) Have you tried running NONMEM 6 w/ gfortran? Claus in his email below
seems to have tried it.
3) Would you be able to share info on the (32- or 64-bit) fortran
compiler build configuration and additional fortran related libraries
needed for them to work with SGE, and Linux servers? Are any fortran
libraries are needed for communication between Fortran compiler and SGE?
4) What kind of master-slave configuration is being used? Do you have
any redundancy in place? e.g., what happens if the "master" machine is
down?
5) What do your scripts do on the cluster?
Thanks so much for taking time.
Best Regards,
Naren
-----Original Message-----
From: Elassaiss - Schaap, J.
[mailto:jeroen.elassaiss
Sent: Wednesday, September 30, 2009 11:15 PM
To: Narayanan, Naren
Cc: owner-nmusers
Subject: RE: Antwort: [NMusers] Install NONMEM on Linux cluster
Hi Naren,
We have NONMEM VI installed with nmqual and run it with PsN on a SGE
controlled cluster with intel quadcores (and R, xpose etc.). The nonmem
installation and the run directories are all on shared drives. We have
found no problems running via PsN on SGE.
Of it all, the trickiest part was the installation of Nonmem on linux
_with_ nmqual while enabling PsN. Installation without nmqual on the
other hand is no problem. trapfpe.c has been compiled in, see g77 info
pages. Our compiler options: "-W -O2 /apps/.../trapfpe.o"
I have written some simple scripts to make running on our cluster a bit
easier, please contact me if you are interested or if you need some more
details.
Best regards,
Jeroen
Jeroen Elassaiss-Schaap, PhD
Modeling & Simulation Expert
Pharmacokinetics, Pharmacodynamics & Pharmacometrics (P3)
Early Clinical Research and Experimental Medicine
Schering-Plough Research Institute
T: +31 41266 9320
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.
Hi Naren,
ad 1: Will look them up later on. IIRC nothing special was needed for
g77 in nmqual. The largest chance was needed in PsN, actually. There
some code was added to use the nmqual's 'OUTPUT' filename rather than
the redirection that is configured by nonmem's SETUP
ad 2: We have not tried gfortran (yet)
ad 3: Nothing special was needed next to the standard configuration of
our cluster machines. SGE does not require special libraries, all
operations are performed on OS-level. Except checkpointing (and perhaps
other advanced options), but we never tried that.
ad 4: There is one back-up headnode.
ad 5: One script takes a commandline and submits it to the cluster with
preconfigured options, including e-mail notification. I also have
scripts that do clean-up of psn folders, help with updating of
run-numbers in control streams, automatically draw parameter draws from
the covariance matrix and one that does more detailed diagnostics on the
covariance matrix.
You are welcome!
Best regards,
Jeroen
Jeroen Elassaiss-Schaap, PhD
Modeling & Simulation Expert
Pharmacokinetics, Pharmacodynamics & Pharmacometrics (P3)
Early Clinical Research and Experimental Medicine
Schering-Plough Research Institute
T: +31 41266 9320
PS: I only realized later on that these mails never made it to the list,
excuse me for that.
Quoted reply history
________________________________
From: Narayanan, Naren [mailto:[email protected]]
Sent: Friday, 02 October, 2009 3:20
To: Elassaiss - Schaap, J. (Jeroen)
Subject: RE: Antwort: [NMusers] Install NONMEM on Linux cluster
Hi Jeroen,
Thanks for your response.
1) Would you be able to share the g77 related changes made in NMQual's
xml files for successful installation with PsN and SGE? We installed NM6
using NMQual (without SGE and PsN). By the way, thanks for reminding
about trapping floating point errors! I would use that option too.
2) Have you tried running NONMEM 6 w/ gfortran? Claus in his email below
seems to have tried it.
3) Would you be able to share info on the (32- or 64-bit) fortran
compiler build configuration and additional fortran related libraries
needed for them to work with SGE, and Linux servers? Are any fortran
libraries are needed for communication between Fortran compiler and SGE?
4) What kind of master-slave configuration is being used? Do you have
any redundancy in place? e.g., what happens if the "master" machine is
down?
5) What do your scripts do on the cluster?
Thanks so much for taking time.
Best Regards,
Naren
-----Original Message-----
From: Elassaiss - Schaap, J. (Jeroen)
[mailto:[email protected]]
Sent: Wednesday, September 30, 2009 11:15 PM
To: Narayanan, Naren
Cc: [email protected]
Subject: RE: Antwort: [NMusers] Install NONMEM on Linux cluster
Hi Naren,
We have NONMEM VI installed with nmqual and run it with PsN on a SGE
controlled cluster with intel quadcores (and R, xpose etc.). The nonmem
installation and the run directories are all on shared drives. We have
found no problems running via PsN on SGE.
Of it all, the trickiest part was the installation of Nonmem on linux
_with_ nmqual while enabling PsN. Installation without nmqual on the
other hand is no problem. trapfpe.c has been compiled in, see g77 info
pages. Our compiler options: "-W -O2 /apps/.../trapfpe.o"
I have written some simple scripts to make running on our cluster a bit
easier, please contact me if you are interested or if you need some more
details.
Best regards,
Jeroen
Jeroen Elassaiss-Schaap, PhD
Modeling & Simulation Expert
Pharmacokinetics, Pharmacodynamics & Pharmacometrics (P3)
Early Clinical Research and Experimental Medicine
Schering-Plough Research Institute
T: +31 41266 9320
This message and any attachments are solely for the intended recipient. If you
are not the intended recipient, disclosure, copying, use or distribution of the
information included in this message is prohibited --- Please immediately and
permanently delete.