From owner-chemistry@ccl.net Mon Sep 18 06:02:00 2017 From: "Maria Dimitrova maria.dimitrova-x-helsinki.fi" To: CCL Subject: CCL:G: Disk space error in DoCrtU when optimizing geometry in Gaussian Message-Id: <-53005-170918053215-8288-ImJI+MLUsLk8Ad/+oL+cbA*server.ccl.net> X-Original-From: "Maria Dimitrova" Date: Mon, 18 Sep 2017 05:32:12 -0400 Sent to CCL by: "Maria Dimitrova" [maria.dimitrova*o*helsinki.fi] Hello, I have a fairly big molecule, the structure of which I would like to optimise in Gaussian 16.03. The calculation crashes with the error message "Not enough space in DoCrtU". It does not mention memory, so I guess this refers to disk space instead of RAM memory. How can I specify another scratch directory? Do I need to give a certain amount of disk space when I submit the job through SLURM? Best regards, Maria Dimitrova Email: maria.dimitrova * helsinki.fi From owner-chemistry@ccl.net Mon Sep 18 08:17:00 2017 From: "Guzman, Francisco fg58[#]njit.edu" To: CCL Subject: CCL:G: Disk space error in DoCrtU when optimizing geometry in Gaussian Message-Id: <-53006-170918081558-4712-ix6KYsfe/XlYGoO336yo6A%x%server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="001a113a0d62288564055975b449" Date: Mon, 18 Sep 2017 08:15:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58]=[njit.edu] --001a113a0d62288564055975b449 Content-Type: text/plain; charset="UTF-8" I think you can specify multiple scratch directories byt having multiple RWF files. Try adding something similar to your input file %rwf=/scratch-dir/file1.rwf, 1900MB, /scratch-dir/file2.rwf, 1900MB, /scratch-dir/file3.rwf,1900MB In this example, 1900MB * 3 = 5,700 MB of scratch space is used. Not sure what SLURM is, but as long as you have read/write permission in a directory you can use as scratch, this should work. Else, contact your local IT Gods. On Mon, Sep 18, 2017 at 5:32 AM, Maria Dimitrova maria.dimitrova-x-helsinki.fi wrote: > > Sent to CCL by: "Maria Dimitrova" [maria.dimitrova*o*helsinki.fi] > Hello, > > I have a fairly big molecule, the structure of which I would like to > optimise in Gaussian 16.03. The calculation crashes with the error message > "Not enough space in DoCrtU". It does not mention memory, so I guess this > refers to disk space instead of RAM memory. How can I specify another > scratch directory? Do I need to give a certain amount of disk space when I > submit the job through SLURM? > > Best regards, > Maria Dimitrova > > Email: > maria.dimitrova * helsinki.fi> > > -- Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology --001a113a0d62288564055975b449 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I think you can specify multiple scratch directo= ries byt having multiple RWF files. Try adding something similar to your in= put file

%rwf=3D/scratch-dir/file1.rwf, 1900MB, /scratch-dir/f= ile2.rwf, 1900MB, /scratch-dir/file3.rwf,1900MB

I= n this example, 1900MB * 3 =3D 5,700 MB of scratch space is used.

Not sure what SLURM is, but as long as you have read/write= permission in a directory you can use as scratch, this should work. Else, = contact your local IT Gods.

On Mon, Sep 18, 2017 at 5:32 AM, Maria Dimitrova maria.dimitrova-x-helsinki.fi <owner-chemistry|a|ccl.net> wrote:

Sent to CCL by: "Maria=C2=A0 Dimitrova" [maria.dimitrova*o*helsinki.fi]
Hello,

I have a fairly big molecule, the structure of which I would like to optimi= se in Gaussian 16.03. The calculation crashes with the error message "= Not enough space in DoCrtU". It does not mention memory, so I guess th= is refers to disk space instead of RAM memory. How can I specify another sc= ratch directory? Do I need to give a certain amount of disk space when I su= bmit the job through SLURM?

Best regards,
Maria Dimitrova

Email:
maria.dimitrova * helsinki.fi



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--
Francisco Guzman<= /span>
PhD Candidate
Otto H. York Department of Che= mical, Biological and Pharmaceutical Engineering
New Jersey Institute of= Technology
--001a113a0d62288564055975b449-- From owner-chemistry@ccl.net Mon Sep 18 09:04:01 2017 From: "Andrew Dalke dalke!A!dalkescientific.com" To: CCL Subject: CCL: chemfp 1.3 released Message-Id: <-53007-170918085133-15914-VCjg7WvqRuSdtEA8cdS1Bw|*|server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 18 Sep 2017 14:51:26 +0200 Mime-Version: 1.0 (Mac OS X Mail 10.2 \(3259\)) Sent to CCL by: Andrew Dalke [dalke-*-dalkescientific.com] Dear CCL subscribers, chemfp 1.3 is now available from http://dalkescientific.com/releases/chemfp-1.3.tar.gz . Chemfp is a set of command-line tools and a Python library for working with cheminformatics fingerprints. It can use OEChem/OEGraphSim, RDKit, or Open Babel to create fingerprints in the FPS format, and it implements a high-speed Tanimoto search. The software is available under the MIT license. For more information see http://chemfp.com/ . Documentation is available from http://chemfp.readthedocs.io/en/chemfp-1.3/ . There are many changes over chemfp 1.1, which was the last release of the public/no-cost version of chemfp. The biggest ones are: - Tested against the current version of all of the chemistry toolkits, as well as older versions from the last couple of years - Added support for the Avalon and pattern fingerprints in RDKit - In-memory Tanimoto searches for 166-bit MACCS keys on computers with the POPCNT instruction is about 30% faster. - FPS loading is about 40% faster. As a result, file-based searches are about 25% faster. - The in-memory search algorithms in version 1.1 were parallelized with OpenMP, but the NxM k-nearest search was left out. That case is now also parallelized. - Some of the APIs from the commercial version were backported to 1.3, including the fingerprint writer API and functions for substructure fingerprint screening. - Added and improved docstrings This release support Python 2.7 but it no longer supports Python 2.5 or Python 2.6. Best regards, Andrew Dalke dalke+/-dalkescientific.com