From owner-chemistry@ccl.net Sat Sep 10 00:08:45 2005 From: "CCL" To: CCL Subject: CCL: Molpro and memory Message-Id: <-29117-050909235513-20231-DUcROUZqAAanpwYwt3FuqA|"|server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 09 Sep 2005 23:00:32 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf|"|helix.nih.gov] I seem to remember reading about 1Gb limit per single process too, though I can't find the reference now. This is what Linus had said about the issue - according to him, it's more like 3Gb limit, but not all of it can be accessible - due to shared libs taking space etc. You need to move to 64-bit cpu. http://www.ussg.iu.edu/hypermail/linux/kernel/9801.2/0194.html Igor On Fri, 2005-09-09 at 19:04, CCL wrote: > Sent to CCL by: "Ben Swerts" [ben.swerts/./ua.ac.be] > > > Hi Alexander, > > I have absolutely no experience with Molpro but I can tell you this: > When using GCC as the compiler in 32 bit mode, I noticed a limit of 1 GB for > statically allocated memory when compiling fortran codes. I tried a lot of > things to circumvent this problem but never succeeded. Now we have 64 bit > machines and this 1 GB limit is finally a thing of the past. > I guess the problem is related to Linux. Applications just crash when > compiled with more than 1 GB. > > Greetz, > > > Ben > > > -----Original Message----- > > From: owner-chemistry|"|ccl.net [mailto:owner-chemistry|"|ccl.net] > > Sent: Friday, September 09, 2005 10:44 PM > > To: Swerts, Ben > > Subject: CCL: Molpro and memory > > > > > > Sent to CCL by: Alexander Martins Silva [alex.msilva---uol.com.br] > > > > Hi, > > > > This is my second message about the same issue: > > Molpro and memory. I've compiled the Molpro in a Xeon > > machine with 2 proc and 4 GB of memory. However, I couldn't > > use more than 1Gb of memory when executing jobs. I've > > already expanded the kernel.shmall and kernel.shmmax > > parameters up to 2Gb and nothing happens. The manual don't > > tell me nothing about this subject. Is it a problem related > > to the Intel Fotran Compiler? Anybody could help me? > > > > > > Thanks in advance, > > > > Alexander.> From owner-chemistry@ccl.net Sat Sep 10 09:52:14 2005 From: "CCL" To: CCL Subject: CCL: Need coordinates of carbon clusters Message-Id: <-29118-050910080309-27157-DUcROUZqAAanpwYwt3FuqA+*+server.ccl.net> X-Original-From: "Muneerah" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="windows-1256" Date: Sat, 10 Sep 2005 12:50:36 +0300 MIME-Version: 1.0 Sent to CCL by: "Muneerah" [mmogren+*+ksu.edu.sa] Hi all: I am looking for coordinates of some carbon clusters which has more than 20 atoms. Does anyone know a cite where I can find these coordinates. Does anyone know a program that generates these clusters, not necessarily calculate their energy. Thanks a lot. Muneerah From owner-chemistry@ccl.net Sat Sep 10 19:48:19 2005 From: "CCL" To: CCL Subject: CCL: Doing PDB modeling on your Pocket PC - PDB.IH Message-Id: <-29119-050910165917-5308-DUcROUZqAAanpwYwt3FuqA ~~ server.ccl.net> X-Original-From: e-Chemistry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 10 Sep 2005 13:59:12 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: e-Chemistry [echemistry ~~ yahoo.com] Another software running on your Pocket PC - PDB.IH. Features include: online downloading PDB; locally caching PDB; viewing PDB summary; viewing 3D PDB pictures, viewing PDB hierarchy; viewing secondary structure etc. http://chemih.com/pdb.ih/ We are still experiencing that problem for ChemIH. It's expected to be solved in one or two weeks. We appreciate your patience. ______________________________________________________ Click here to donate to the Hurricane Katrina relief effort. http://store.yahoo.com/redcross-donate3/ From owner-chemistry@ccl.net Sat Sep 10 23:33:34 2005 From: "CCL" To: CCL Subject: CCL: Molpro and memory Message-Id: <-29120-050910203108-19878-DUcROUZqAAanpwYwt3FuqA{=}server.ccl.net> X-Original-From: Kirk Peterson Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sat, 10 Sep 2005 16:33:55 -0700 Mime-Version: 1.0 Sent to CCL by: Kirk Peterson [kipeters{=}wsu.edu] Perhaps this is due to using gcc, but with the Portland Group compiler we consistently allocate more than 1 GB of memory (up to 2) with molpro on our 32-bit athlon cluster (dual node, 3GB RAM, 4GB of swap). Is your kernel compiled with large memory support? -Kirk On Fri, Sep 09, 2005 at 11:00:32PM -0400, CCL wrote: > > Sent to CCL by: "Igor Filippov [Contr]" [igorf|"|helix.nih.gov] > I seem to remember reading about 1Gb limit per single process too, > though I can't find the reference now. This is what Linus had said about > the issue - according to him, it's more like 3Gb limit, but > not all of it can be accessible - due to shared libs taking space etc. > You need to move to 64-bit cpu. > > http://www.ussg.iu.edu/hypermail/linux/kernel/9801.2/0194.html > > Igor > > > On Fri, 2005-09-09 at 19:04, CCL wrote: > > Sent to CCL by: "Ben Swerts" [ben.swerts/./ua.ac.be] > > > > > > Hi Alexander, > > > > I have absolutely no experience with Molpro but I can tell you this: > > When using GCC as the compiler in 32 bit mode, I noticed a limit of 1 GB for > > statically allocated memory when compiling fortran codes. I tried a lot of > > things to circumvent this problem but never succeeded. Now we have 64 bit > > machines and this 1 GB limit is finally a thing of the past. > > I guess the problem is related to Linux. Applications just crash when > > compiled with more than 1 GB. > > > > Greetz, > > > > > > Ben > > > > > -----Original Message----- > > > From: owner-chemistry{=}ccl.net [mailto:owner-chemistry{=}ccl.net] > > > Sent: Friday, September 09, 2005 10:44 PM > > > To: Swerts, Ben > > > Subject: CCL: Molpro and memory > > > > > > > > > Sent to CCL by: Alexander Martins Silva [alex.msilva---uol.com.br] > > > > > > Hi, > > > > > > This is my second message about the same issue: > > > Molpro and memory. I've compiled the Molpro in a Xeon > > > machine with 2 proc and 4 GB of memory. However, I couldn't > > > use more than 1Gb of memory when executing jobs. I've > > > already expanded the kernel.shmall and kernel.shmmax > > > parameters up to 2Gb and nothing happens. The manual don't > > > tell me nothing about this subject. Is it a problem related > > > to the Intel Fotran Compiler? Anybody could help me? > > > > > > > > > Thanks in advance, > > > > > > Alexander.> > > -- --------------------- Kirk A. Peterson Professor of Chemistry and Materials Science Washington State University Pullman, WA 99164-4630 kipeters{=}wsu.edu (509) 335-7867 http://tyr0.chem.wsu.edu/~kipeters