From owner-nwchem-users@emsl.pnl.gov Wed Jun 6 07:54:37 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l56EsZZs003874 for ; Wed, 6 Jun 2007 07:54:36 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l56EsZLJ003873 for nwchem-users-outgoing-0915; Wed, 6 Jun 2007 07:54:35 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: OK_Domains X-Ironport-SBRS: 4.1 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AgAAAKNnZkZCxGTojWdsb2JhbACPXgIBAQcIBAkGHw X-IronPort-AV: E=Sophos;i="4.16,390,1175497200"; d="scan'208";a="34143663" DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; b=HO30FI0hMIDaQghScpWdatwvKkzHggTz81zBSTTTLCNRFJ6lyaDcEDjdx3xoog9LHeYEWi3Kgh5z3lQC8uzQ9oxSFAMOuIqw63UVrq42YE+Ks3LlGWoYQ9nWr1wPsUepICy/POEcxY/hsmxlOblGXj6fXfuGIPU99PHdUII9j+Y=; X-YMail-OSG: mbvhvf0VM1kSDdVa5V1qFN2isUvA.b0ChbmAxzbnSG2vM7KoLD15I9f6Veh4t1_UPA-- Date: Wed, 6 Jun 2007 07:54:31 -0700 (PDT) From: Francesco Pietra Subject: [NWCHEM] No output file on restart To: users nwchem MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Message-ID: <380267.12951.qm@web58903.mail.re1.yahoo.com> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Bert: Perhaps I have hidden the problem. The DFT/Geom procedure was restarted successfully by adding in nwch.nw the block you indicated below. However, I must have missed some indication in the launching command parallel nwchem nwch.nw The outcome was seen in the screen, and I believe that the computation has ended successfully. Though, contrary to my expectations nwch.nwout was not overwritten and, as indicated below, there was no useful text file written. Surely I did that wrongly. Now, is it possible to restart the restarted computation (resulting files indicated below) just to save time for this rather demanding process (98-atoms molecule). Thanks francesco pietra --- Francesco Pietra wrote: > Date: Sat, 2 Jun 2007 21:35:59 -0700 (PDT) > From: Francesco Pietra > Subject: Fwd: RE: [NWCHEM] Failure in restart > To: users nwchem > > According to the screen from where the restart was > launched, the calculation probably ended positively > (I > see only the list of names of NW developers, no note > about errors0) Though I am unable to see where the > output is. That screen can't back explored, and the > only new text files written are > > *.grinfo.0 > *grinfo.1 > *.grinfo2 > *.grinfo3 > > the non text files written are > > *.b > *.b^-1 > *.db > *.c > *.p > *.zmat > *.gridpts.0 > *.gridpts1 > *.gridpts2 > *.gridpts3 > > > Part of the problem of scarcity of disk space was > due > to .trash containing many file. > > Help. > Thanks > > francesco pietra > --- Francesco Pietra wrote: > > > Date: Sat, 2 Jun 2007 09:18:58 -0700 (PDT) > > From: Francesco Pietra > > Subject: Fwd: RE: [NWCHEM] Failure in restart > > To: users nwchem > > > > Please, disregard the original notes below. > Failure > > was due to launching the "restart" in serial mode, > > while the available vectors had been obtained from > > computation in parallel mode. > > > > That said, and apologized about, two related > > questions: > > > > 1) Should a restarted DFT/Geom (like present one) > > die, > > or be deliberately killed, could it be restarted > > again? If so, does the second restarted procedures > > make use of the computation during the first > > restart, > > or does it start again from the original vectors? > > > > 2) This restarted procedure makes heavier use of > the > > swap that the original procedure (of the 97GB > > available, the original computation used no more > > than > > 70%, while the restarted procedure uses 90-100%, > > according to "df -h", with a few MB free). > > Therefore, > > what happens if the swap becomes insufficient? For > > the > > moment it goes on expedite, the bad situation of > the > > swap notwithstanding (I have in mind to add a > second > > raid 1 array of HDs, just for the swap; > > unfortunately > > the nvidias do not like cheap HDs, which result in > > blurring the memory). > > > > Thanks > > francesco pietra > > > > > > > > --- Francesco Pietra > wrote: > > > > > Date: Sat, 2 Jun 2007 00:03:47 -0700 (PDT) > > > From: Francesco Pietra > > > Subject: RE: [NWCHEM] Failure in restart > > > To: "DeJong, Wibe A" , > > > users nwchem > > > > > > Bert: > > > Unfortunately, it did not work. > > > > > > I have tried also changing the Title from > > > "eqax77834.m052x-1" to > > "eqax77834m052x-1-restarted" > > > (in any case starting from a fresh copy of the > > whole > > > directory from the original calculation). > > > > > > The restart procedure begun by using the old > > > vectors, > > > though top (i option) showed that only one > > processor > > > was being used. That situation lasted for a long > > > time, > > > then I left running overnight, finding in the > > > morning > > > on the screen: > > > > > > xlm_ao_mo: tmp1 806484 > > > Current input line > > > 17: task dft optimize > > > > > > see manual for more information > > > > > > For further details see manual section > > > 0:0:xlm_ao_mo: tmp1::806484 > > > Last System Error Message from Task 0: > > > Inappropriate iotcl for device > > > ARMCI aborting 886484 (0xc4c84) > > > > > > Nothing new was written (as far as I could see) > in > > > the > > > directory for this calculation. > > > > > > Recently I carried out successfully the same > > > calculation for a diastereomer of present > > molecule. > > > > > > I have now tried a RHF/Geometry/6-31G* for > > > cyclopentane, launched from ECCE to the remote > > > machine > > > were the above calculations have been carried > out. > > > It > > > was performed OK, all nodes were involved (top, > i > > > option). > > > > > > The only solution I can see, is to take the last > > > Cartesian coordinates from the original > nwch.nwout > > > stopped at 50 iter, start a new DFT to let > nwchem > > > doing a new guess Hessian. I'll do nothing, > > however, > > > until you have the opportunity to read these > > notes. > > > > > > Thanks > > > > > > francesco > > > > > > --- "DeJong, Wibe A" > wrote: > > > > > > > Francesco, > > > > > > > > You specified 50 steps in the geometry > > > optimization > > > > and that's why it > > > > stopped in the first run. Note, not just the > > Gmax > > > > and Grms need to be > > > > converged, the Xmax and Xrms need to be within > > the > > > > threshold too. > > > > > > > > As to your restart. Try adding back in the > > > following > > > > block before the > > > > task line > > > > > > > > dft > > > > mult 1 > > > > XC m05-2x > > > > iterations 100 > > > > mulliken > > > > end > > > > > > > > Thanks, > > > > > > > > Bert de Jong > > > > NWCHem developer > > > > > > > > -----Original Message----- > > > > From: owner-nwchem-developers@emsl.pnl.gov > > > > [mailto:owner-nwchem-developers@emsl.pnl.gov] > On > > > > Behalf Of Francesco > > > > Pietra > > > > Sent: Wednesday, May 30, 2007 11:57 PM > > > > To: users nwchem > > > > Subject: [NWCHEM] Failure in restart > > > > > > > > I wonder whether I did some silly error. > > > > > > > > 1)I submitted a dft/geometry according to > > attached > > > > file dft_input (made > > > > shorter by removing most coordinates for the > > > > 98-atoms molecule). > > > > > > > > The calculation on 4 nodes 4GB/node went on > > > > regularly. > > > > At iteration 50, Gmax and Grms were already > OK > > > > (default converge > > > > criteria). However, it crashed at this stage. > > The > > > > tail of nwch.nwout is > > > > attached (dft_tail). > > > > > > > > The calculation was restarted by editing > nwch.nw > > > > and, sitting in the dir > > > > for all output files for this calculation, > > > > launching: > > > > > > > > $ /home/francesco/nwchem50/bin/nwchem nwch.nw > > > > > > > > where the edited input nwch.nw is attached > > > > (dft_input_restart). > > > > > > > > It aborted soon with error: > > > > > > > > > > > > grid_nbfm: silly accgauss > > > > > > > > current input line: > > > > 7: task optimize > > > > > > > > This error has not yet been assigned. > > > > > > > > 0:0: grid_nbfm: silly accgauss:: 0 > > > > > > > > Last System error message from task 0: > > > Inappropriate > > > > ioctl for device > > > > ARMCI aborting 0. > > > > > > > > > > > > > > > > The existing nwch.nwout from original > > calculation > > > > has not been > > > > rewritten. At any event, before setting up the > > > > restart procedure, I had > > > > saved on external HD a copy of the whole > > directory > > > > for this calculation. > > > > > > > > Hope to have made the issue clear. > > > > > > > > Thanks > > > > francesco pietra > > > > > > > > > > > > > > > > > > > > > > ________________________________________________________________________ > > > > ____________Boardwalk for $500? In 2007? Ha! > > Play > > > > Monopoly Here and Now > > > > (it's updated for today's economy) at Yahoo! > > > Games. > > > > > > > > > > http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > Food fight? Enjoy some healthy debate > > > in the Yahoo! 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