From owner-nwchem-users@emsl.pnl.gov Sat Jun 2 21:36:06 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 l534a5cW025410 for ; Sat, 2 Jun 2007 21:36:06 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l534a4eh025409 for nwchem-users-outgoing-0915; Sat, 2 Jun 2007 21:36:04 -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: 4.0 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: Ao8CAA3iYUZCxGTqjGdsb2JhbAAVj24BAQEICAQPH4oa X-IronPort-AV: i="4.16,377,1175497200"; d="scan'208"; a="21728934:sNHT21476035" 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=fPLBvtZffWtiehdfA7m/sZ+WXN0kHVdjLBGiZVPDvZphF1cpBAjjjEezExBXIi/vehl1zxhTewiB5X4szpEdONX6sHA8FAym7FzhNA6qAc2ODpKNMiejFNWmwWJlDN/N8pmf9OVl/2rITQWAgrqzBwnltR18XDkVUiEMSPPxtUE=; X-YMail-OSG: AlTO5usVM1kmNERFrGalLhqCnwsO8U2Om2XIcNAki6_4B0RJJBbla05m7o9RU9dOjGwrqVVcqMS0jTYc1ni00iygC4kpc594yOO1 Date: Sat, 2 Jun 2007 21:35:59 -0700 (PDT) From: Francesco Pietra Subject: Fwd: RE: [NWCHEM] Failure in restart To: users nwchem MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Message-ID: <622599.32836.qm@web58905.mail.re1.yahoo.com> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk 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! Answers Food & Drink Q&A. > > > http://answers.yahoo.com/dir/?link=list&sid=396545367 > > > > > > > ____________________________________________________________________________________ > Fussy? Opinionated? Impossible to please? 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