From owner-chemistry@ccl.net Sat May 6 15:00:00 2006 From: "dedey%x%alumni.bilkent.edu.tr" To: CCL Subject: CCL: Summ. GAMESS AMD 64 Linking & a strange new situation Message-Id: <-31698-060506145701-3272-IyYvZceRebjWImuKK6BqgQ/./server.ccl.net> X-Original-From: Date: Sat, 06 May 2006 21:56:52 EEST Sent to CCL by: [dedey:+:alumni.bilkent.edu.tr] Hi all, This is a summary about GAMESS compilation on AMD 64 pc running FC 4. !!!PLEASE PAY ATTENTION TO THE FUNNY SITUATION AFTER THE COMMENTS OF THE MEMBERS!!! My specific problem was ill activation of one of the source files. Although I specified the true targets (AMD 64) unport.src which has machine dependent codes was not activated.(I still wonder why) When I activated it manually by replacing all *AMD characters with blanks I could link it succesfully. So I managed as follows: 1. manually changed syntax errors of prppop.src (refer to GAMESS mailing list) 2. followed the instructions of readme.unix file 3. manually erased all *AMD characters in unport.src and formed the object unport.o manually normally this part is done by the compall script which calls actvate.x for activation accoarding to the specific target 4. compiled and linked using pgi without any error 5. configured the rungms & runall scripts, tested all input files. all tests were performed succesfully I thank to whom participated. BELOW ARE COMMENTS FROM THEM ************************************************************************ Brian Salter-Duke It looks to me as if you need to address machine specific stuff in unport.src. Those missing objects early in the lked output may be important. ************************************************************************ zhendong zhao zzhao . olemiss.edu Hi, As I said in the previous email, the updated version has some errors in source code. in prppop.src, the > should be .GT.. == should be .EQ.. After I correct these errors, I can successfully compile the updated version gamess for AMD64 with PGI x64 verion even without changing any scripts. This error is mentioned by others in gamess email list. ************************************************************************ Xiaojian Mao what is exactly your linking problem? a lot of undefined symboles? Normally you should search all library files in your machine to find out which library you should include. In my case, I found all those symbols in the "libgcc_eh.a" library file. Adding paramter "-lgcc_eh" to the link source code solved the problem. ************************************************************************ THE FUNNY THING IS: I tested the performances of 32 bit and 64 bit GAMESS executables on the 64 bit AMD pc. In most cases 64 bit executable runs faster but with the CR-CC job employing TZV basis 64 bit executable cannot finish the job whereas 32 bit exe does succesfully. Inputs are same for both jobs and given below. $CONTRL RUNTYP=energy CCTYP=CR-CC $END $BASIS GBASIS=tzv $END $CONTRL ISPHER=1 $END $BASIS NDFUNC=2 NFFUNC=1 NPFUNC=1 POLAR=POPN311 $END $CONTRL NOSYM=1 $END $system mwords=460 $end I here give the related parts from the log files, 64 bit one cannot pass the point below but 32 bit finishes succesfully. **** BELOW IS WHERE AMD 64 INCOMPLETE JOB GETS STUCK*** COUPLED CLUSTER CALCULATION --------------------------- CCTYP =CR-CC TOTAL NUMBER OF MOS = 222 NUMBER OF OCCUPIED MOS = 21 NUMBER OF FROZEN CORE MOS = 6 NUMBER OF FROZEN VIRTUAL MOS = 0 MAXIMUM CC ITERATIONS = 30 MAXIMUM DIIS ITERATIONS = 5 CONVERGENCE CRITERION FOR CC = 7 AMPLITUDE ACCURACY THRESHOLD = 0.0E+00 ------------------------------- PARTIAL INTEGRAL TRANSFORMATION ------------------------------- NUMBER OF CORE MOLECULAR ORBITALS = 6 NUMBER OF OCCUPIED MOLECULAR ORBITALS = 222 TOTAL NUMBER OF MOLECULAR ORBITALS = 222 TOTAL NUMBER OF ATOMIC ORBITALS = 252 THRESHOLD FOR KEEPING TRANSFORMED 2E- INTEGRALS = 1.000E-09 AO INTEGRALS WILL BE READ IN FROM DISK... EVALUATING THE FROZEN CORE ENERGY... ----- FROZEN CORE ENERGY = -294.1883029370 # OF WORDS AVAILABLE = 460000000 # OF WORDS NEEDED = 1735561322 FOR IN MEMORY TRANSFORMATION FOR THE SEGMENTED TRANSFORMATION: MINIMUM= 8411282 WORDS FOR 1 MOLECULAR ORBITAL PER PASS MAXIMUM=1735561322 WORDS FOR ALL MOLECULAR ORBITALS IN 1 PASS ( 8033256 EXTRA WORDS WOULD INCLUDE AN EXTRA ORBITAL/PASS) SEGMENTED PARTIAL TRANSFORMATION WOULD USE 434173850 WORDS, DISTRIBUTING 4 PASSES EACH CONTAINING 54 ORBITALS OVER 1 PROCESSORS. CHOOSING SEGMENTED PARTIAL TRANSFORMATION... PASS # 1 TOOK 496.02 SECONDS. PASS # 2 TOOK 581.45 SECONDS. **************** stuck in pass # 3 ????? ***************** DDI Process 0: trapped a segmentation fault (SIGSEGV). ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). **** HERE STARTS PARTIAL 32 BIT LOG FILE **** **** 32 BIT JOB PASSES THIS PART AND COMPLETES THE CALCULATION SUCCESFULLY *** --------------------------- COUPLED CLUSTER CALCULATION --------------------------- CCTYP =CR-CC TOTAL NUMBER OF MOS = 222 NUMBER OF OCCUPIED MOS = 21 NUMBER OF FROZEN CORE MOS = 6 NUMBER OF FROZEN VIRTUAL MOS = 0 MAXIMUM CC ITERATIONS = 30 MAXIMUM DIIS ITERATIONS = 5 CONVERGENCE CRITERION FOR CC = 7 AMPLITUDE ACCURACY THRESHOLD = 0.0E+00 ------------------------------- PARTIAL INTEGRAL TRANSFORMATION ------------------------------- NUMBER OF CORE MOLECULAR ORBITALS = 6 NUMBER OF OCCUPIED MOLECULAR ORBITALS = 222 TOTAL NUMBER OF MOLECULAR ORBITALS = 222 TOTAL NUMBER OF ATOMIC ORBITALS = 252 THRESHOLD FOR KEEPING TRANSFORMED 2E- INTEGRALS = 1.000E-09 AO INTEGRALS WILL BE READ IN FROM DISK... EVALUATING THE FROZEN CORE ENERGY... ----- FROZEN CORE ENERGY = -294.1883029370 # OF WORDS AVAILABLE = 460000000 # OF WORDS NEEDED = 1735529570 FOR IN MEMORY TRANSFORMATION FOR THE SEGMENTED TRANSFORMATION: MINIMUM= 8379530 WORDS FOR 1 MOLECULAR ORBITAL PER PASS MAXIMUM=1735529570 WORDS FOR ALL MOLECULAR ORBITALS IN 1 PASS ( 8033256 EXTRA WORDS WOULD INCLUDE AN EXTRA ORBITAL/PASS) SEGMENTED PARTIAL TRANSFORMATION WOULD USE 434142098 WORDS, DISTRIBUTING 4 PASSES EACH CONTAINING 54 ORBITALS OVER 1 PROCESSORS. CHOOSING SEGMENTED PARTIAL TRANSFORMATION... PASS # 1 TOOK 576.36 SECONDS. PASS # 2 TOOK 723.19 SECONDS. PASS # 3 TOOK 787.56 SECONDS. **************** pass # 3 is done ???? ***************** PASS # 4 TOOK 770.50 SECONDS. TOTAL NUMBER OF TRANSFORMED 2E- INTEGRALS KEPT = 274367375 ... END OF INTEGRAL TRANSFORMATION ... STEP CPU TIME = 2876.01 TOTAL CPU TIME = 3208.6 ( 53.5 MIN) TOTAL WALL CLOCK TIME= 4414.7 SECONDS, CPU UTILIZATION IS 72.68% ******************************************************************************************** So I am confused about if recompiling GAMESS with some other parameters will solve the problem or not. Is there a way to skip such erroneous parts with change in the input. Why not the 64 bit executable cannot write the files on the disk where the 32 bit one does. The flow of the calculation as seen from the output is exactly the same for both. The error is a segmentation fault but if someone asks about disk space it is not a problem, there is more than 200 gb free space. The double precision to single thing when moving from 32 to 64 bit architecture is said to be done with the compilation scripts of GAMESS. The identical # OF WORDS AVAILABLE = 460000000 # OF WORDS NEEDED = 1735529570 FOR IN MEMORY TRANSFORMATION messages imply no such single-double precision problem as the amount of memory is the same for both. I also think about swap space... In particular I ask; Can I find the causes by analyzing some specific source files, if yes which? As far as I know there is no way to increase swap space in Linux without repartitioning. If I am mistaken how can I do this? Any other comments? Thanks again... -- Yavuz Dede Comp. Chem. Lab. +90 312 210 3187 METU Ankara From owner-chemistry@ccl.net Sat May 6 15:39:01 2006 From: "Robinson, James James.Robinson:+:evotec.com" To: CCL Subject: CCL: Molden Windows Version? Message-Id: <-31699-060506153743-17562-Dz/DSR6zbs1p1wuH+j+Abw]![server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 6 May 2006 20:37:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson.:.evotec.com] Try these two links for Xserver software... http://x.cygwin.com/ and http://www.labf.com/ . Both work okay with Molden. Shame microsoft don't put a free simple xserver in there software. Hope this helps. James -----Original Message----- > From: owner-chemistry\a/ccl.net [mailto:owner-chemistry\a/ccl.net] Sent: 05 May 2006 02:32 To: Robinson, James Subject: CCL: Molden Windows Version? Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira#%#ist.utl.pt] Young Leh youngleh%gmail.com wrote: > Sent to CCL by: "Young Leh" [youngleh\a/gmail.com] Hi there, > > I downloaded Molden 4.1 for Windows here http://www.cmbi.ru.nl/molden/windowsnt95.html . You must run molden from an X emulator like the one in cygwin. The batch file they provide is intended to run the starnet X emulator. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student -.- IST,Lisbon --http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat May 6 18:38:01 2006 From: "Andreas Bender andreas.bender---complife.org" To: CCL Subject: CCL: Last Call for Papers - CompLife'06 in Cambridge, September 2006 Message-Id: <-31700-060506181744-30640-98BATifLAWO6+3brC2uz7g^server.ccl.net> X-Original-From: "Andreas Bender" Date: Sat, 6 May 2006 18:17:38 -0400 Sent to CCL by: "Andreas Bender" [andreas.bender**complife.org] *** Submission deadline is approaching: 15th May 2006 *** -------------------------------------------------------------- -- LAST CALL FOR PAPERS -- -- CompLife '06 (http://www.complife.org/) -- -------------------------------------------------------------- Following the success of the 1st International Symposium on Computational Life Science in Konstanz in September 2005 The 2nd International Symposium on Computational Life Science is to be held in Cambridge, United Kingdom, on September 27 - 29, 2006 -------------------------------------------------------------- Topics of Interest The focus of the symposium are computational methods for the modeling, analysis and exploration of all aspects of life sciences, ranging from effects on the molecular level to complex interactions networks. Of prime importance for this truly interdisciplinary event will be the integration of the three disciplines Computer Science, Biology, and Chemistry. The program will consist of contributed presentations regarding applicational aspects as well as new theoretical developments. In addition, due to the interdisciplinary nature of the symposium the program will feature not only plenary speakers but also a series of short tutorials introducing relevant areas of the specific research fields to the audience from the respective other fields such as drug discovery, chemical similarity searching, receptor site docking, protein structure prediction, data mining, machine learning, to name a few. Submissions will be reviewed by representatives of all fields to make sure that not only the algorithmic aspects are suited for publication but the application to life science is promising as well. Submissions are sought in (but not limited to) the following areas: Molecular data analysis Systems biology Analysis of heterogenous information sources Human Computer Interaction in Information Mining Computational proteomics Integrative data analysis Statistical data analysis Data mining Molecular simulation Biological networks / Metabolism Molecular informatics Data pipelining Data visualization Large scale chemical computation Data integration/semantics Grid/web services Computer architectures in life sciences The online submission system is open now. The link and further information regarding the submission is available on the conference web site. Student Grants A limited number of Student Grants are available for CompLife 2006: First priority will be given to full-time students who are first authors of papers and present their paper at the conference. Grants are handed out at the conference and will be in the amount of a maximum of EUR500, covering registration, travel, and accommodation. When submitting a paper, students should indicate that they plan to apply for a student grant. Free Life Science Software Session A special session about free software in Life Sciences, where authors can present their programs, will be organised. For more information have a look at the conference web page. -------------------------------------------------------------- Important Dates May 15 Papers due June 26 Notification of acceptance July 10 final papers and sources due Sept 27-29 CompLife '06 Final versions of accepted papers will appear in Springer's Lecture Notes in Bioinformatics (LNBI) Series: http://www.springer.com/sgw/cda/frontpage/0,11855,4-164-2-73658-0,00.html For further information, please refer to the conference website: http://www.complife.org/ -------------------------------------------------------------- From owner-chemistry@ccl.net Sat May 6 19:51:00 2006 From: "Robinson, James James.Robinson=evotec.com" To: CCL Subject: CCL:G: [CCL] RE: G: increasing NStep for partial optimization Message-Id: <-31701-060506194928-26412-vM3/tXIrCgSWsd3ROYoPGA_+_server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 7 May 2006 00:49:27 +0100 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson : evotec.com] -----Original Message----- > From: Robinson, James Sent: 07 May 2006 00:43 To: 'CCL Subscribers'; 'owner-chemistry{=}ccl.net' Subject: RE: G: increasing NStep for partial optimization I have experienced this problem too. The work around I have used is to specify maxcycle with the OPT keyword and then when the run stop because an initial maximum number of cycles have been performed, I then simply insert the RESTART keyword. #p opt=(z-matrix,maxcycle=999) b3lyp/cc-pVDZ nosymm .. Job then dies after a maximum number of steps, related to degrees of freedom. Then change to #p opt=(z-matrix,restart,maxcycle=999) b3lyp/cc-pVDZ nosymm .. And off you go again. Hope this helps. James -----Original Message----- > From: owner-chemistry{=}ccl.net [mailto:owner-chemistry{=}ccl.net] Sent: 04 May 2006 02:54 To: Robinson, James Subject: CCL:G: increasing NStep for partial optimization Sent to CCL by: Sengen Sun [sengensun..yahoo.com] In my experinece, there are often converge problems when one or two constraints are applied between two molecules. Your case appears to me to be such a case, as 100 steps are quite a big number if your system is not very big. A possible indication for this converge problem is oscillating energies in your output files. That is, the energy jumps back and forth without a general trend. I was suggested to do something to deal with this problem. But it is too complicated to me as I had too many systems to be examined. As I spent more and more time in this, I found that this problem depends on different software programs, and sometimes on the levels of computation and basis sets. Some products are simply bad doing this kind of things. A good product for this purpose is Spartan. I am quite amazed at its speed and stability, and never have had this annoying converge problem again since I bought it. The only relationship I have with Wavefunctions, Inc. is my purchase of their product - Spartan. I don't have any other relationships with them, neither am I an advertising agent for them. I just want to clarify that. Sengen ----------------------------- Christopher.DeDobbelaere||student.ua.ac.be wrote: Dear ccl members, I'm doing some popt jobs in g03 where the constraint during the optimization is the distance between two molecules. The optimization takes some time and stops after 100 steps. I already increased maxcycles but that just increases the cycles per scf step. Is there a way to increase NStep to a larger value? This is the error i get: Optimization stopped. -- Number of steps exceeded, NStep= 100 -- Flag reset to prevent archiving. This are the options i'm using right now: p b1b95/6-311+G* popt(MaxCyc=250) freq iop(1/8=10) Thanks in advance! Greetings, Christopher Undergrad. Student University of Antwerp __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt