Tutorial-l Mailing List
From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jun 15 2009 - 08:01:00 CDT
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Anna,
I have to agree with Peter. If for whatever reason one of the precompiled
binaries will not work for you, then I would first try compiling with gcc or
icc. Should these not be viable solutions for whatever reason, then I
would attempt to compile with pgcc.
If you reach the point of compiling with gcc, icc or even pgcc, if it comes
to that, and are still experiencing problems that might require debugging
please let us know. If/when you compile next, and expect potential
problems, it will expediate our search for a solution if you use
"--with-debug" at the end of your "./config ...." command.
Best,
Chris
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Mon, Jun 15, 2009 at 7:12 AM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote: > Hi Anna, > is there any particular reason that you're not using one of the > precompiled binaries? You may need to build your own to get optimal > performance on a cluster eventually, but for the purposes of the > tutorial you may wish to first become familiar with namd using a > known-good version. > > As far as the problem that you're encountering, have you run the tests > that come with charm++ to make sure that you're charm build is working? > You may also want to try building with gcc or icc; we haven't generally > had great experience with the portland group compilers for building NAMD. > > Best, > Peter > > Anna Dejardin wrote: > > Hi Chris, > > > > I'm not sure if this is what you're asking me, but attempting to run > > produced a log file (see below). > > I'm not familiar with the debug flags, how do you use debug? I'm very > > new to Namd and was just trying to run the tutorial simulations, so was > > using the configuration files provided by Namd. > > Let me know if I've misunderstood you. > > > > Anna > > > > Log File: > > > > Info: NAMD 2.6 for Linux-amd64-MPI > > Info: > > Info: Please visit http://www.ks.uiuc.edu/Research/namd/ > > Info: and send feedback or bug reports to namd_at_ks.uiuc.edu > > Info: > > Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005) > > Info: in all publications reporting results obtained with NAMD. > > Info: > > Info: Based on Charm++/Converse 50900 for mpi-linux-amd64 > > Info: Built Wed May 27 12:38:12 BST 2009 by atg on > reinette.lcn.ucl.ac.uk > > Info: 1 NAMD 2.6 Linux-amd64-MPI 1 reinette.lcn.ucl.ac.uk acd > > Info: Running on 1 processors. > > Info: 8096 kB of memory in use. > > Info: Memory usage based on mallinfo > > Info: Changed directory to > > /homes/acd/NAMD2.6/namd-tutorial-files/1-2-sphere > > Info: Configuration file is ubq_ws_eq.conf > > TCL: Suspending until startup complete. > > Info: SIMULATION PARAMETERS: > > Info: TIMESTEP 2 > > Info: NUMBER OF STEPS 0 > > Info: STEPS PER CYCLE 10 > > Info: LOAD BALANCE STRATEGY Other > > Info: LDB PERIOD 2000 steps > > Info: FIRST LDB TIMESTEP 50 > > Info: LDB BACKGROUND SCALING 1 > > Info: HOM BACKGROUND SCALING 1 > > Info: MAX SELF PARTITIONS 50 > > Info: MAX PAIR PARTITIONS 20 > > Info: SELF PARTITION ATOMS 125 > > Info: PAIR PARTITION ATOMS 200 > > Info: PAIR2 PARTITION ATOMS 400 > > Info: MIN ATOMS PER PATCH 100 > > Info: INITIAL TEMPERATURE 310 > > Info: CENTER OF MASS MOVING INITIALLY? NO > > Info: DIELECTRIC 1 > > Info: EXCLUDE SCALED ONE-FOUR > > Info: 1-4 SCALE FACTOR 1 > > Info: DCD FILENAME ubq_ws_eq.dcd > > Info: DCD FREQUENCY 250 > > Info: DCD FIRST STEP 250 > > Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT > > Info: NO VELOCITY DCD OUTPUT > > Info: OUTPUT FILENAME ubq_ws_eq > > Info: BINARY OUTPUT FILES WILL BE USED > > Info: RESTART FILENAME ubq_ws_eq.restart > > Info: RESTART FREQUENCY 500 > > Info: BINARY RESTART FILES WILL BE USED > > Info: SWITCHING ACTIVE > > Info: SWITCHING ON 10 > > Info: SWITCHING OFF 12 > > Info: PAIRLIST DISTANCE 13.5 > > Info: PAIRLIST SHRINK RATE 0.01 > > Info: PAIRLIST GROW RATE 0.01 > > Info: PAIRLIST TRIGGER 0.3 > > Info: PAIRLISTS PER CYCLE 2 > > Info: PAIRLISTS ENABLED > > Info: MARGIN 0 > > Info: HYDROGEN GROUP CUTOFF 2.5 > > Info: PATCH DIMENSION 16 > > Info: ENERGY OUTPUT STEPS 100 > > Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL > > Info: TIMING OUTPUT STEPS 1000 > > Info: PRESSURE OUTPUT STEPS 100 > > Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE > > Info: RADIUS #1 26 > > Info: FORCE CONSTANT #1 10 > > Info: EXPONENT #1 2 > > Info: SPHERE BOUNDARY CENTER(30.3082, 28.805, 15.354) > > Info: LANGEVIN DYNAMICS ACTIVE > > Info: LANGEVIN TEMPERATURE 310 > > Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS > > Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS > > Info: USING VERLET I (r-RESPA) MTS SCHEME. > > Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS > > Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS > > Info: RIGID BONDS TO HYDROGEN : ALL > > Info: ERROR TOLERANCE : 1e-08 > > Info: MAX ITERATIONS : 100 > > Info: RIGID WATER USING SETTLE ALGORITHM > > Info: RANDOM NUMBER SEED 1245054415 > > Info: USE HYDROGEN BONDS? NO > > Info: COORDINATE PDB ../common/ubq_ws.pdb > > Info: STRUCTURE FILE ../common/ubq_ws.psf > > Info: PARAMETER file: CHARMM format! > > Info: PARAMETERS ../common/par_all27_prot_lipid.inp > > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS > > Info: SUMMARY OF PARAMETERS: > > Info: 180 BONDS > > Info: 447 ANGLES > > Info: 566 DIHEDRAL > > Info: 46 IMPROPER > > Info: 6 CROSSTERM > > Info: 119 VDW > > Info: 0 VDW_PAIRS > > Info: **************************** > > Info: STRUCTURE SUMMARY: > > Info: 6682 ATOMS > > Info: 4871 BONDS > > Info: 4074 ANGLES > > Info: 3293 DIHEDRALS > > Info: 204 IMPROPERS > > Info: 74 CROSSTERMS > > Info: 0 EXCLUSIONS > > Info: 6080 RIGID BONDS > > Info: 13966 DEGREES OF FREEDOM > > Info: 2419 HYDROGEN GROUPS > > Info: TOTAL MASS = 41298.8 amu > > Info: TOTAL CHARGE = 1.00955e-06 e > > Info: ***************************** > > Info: Entering startup phase 0 with 8096 kB of memory in use. > > Info: Entering startup phase 1 with 8096 kB of memory in use. > > Info: Entering startup phase 2 with 8096 kB of memory in use. > > Info: Entering startup phase 3 with 8096 kB of memory in use. > > Info: PATCH GRID IS 3 BY 3 BY 3 > > Info: REMOVING COM VELOCITY 0.0863496 -0.00480725 -0.0432049 > > Info: LARGEST PATCH (13) HAS 449 ATOMS > > Info: CREATING 443 COMPUTE OBJECTS > > Info: Entering startup phase 4 with 8096 kB of memory in use. > > Info: Entering startup phase 5 with 8096 kB of memory in use. > > Info: Entering startup phase 6 with 8096 kB of memory in use. > > Measuring processor speeds... Done. > > Info: Entering startup phase 7 with 8096 kB of memory in use. > > Info: CREATING 443 COMPUTE OBJECTS > > Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 > > Info: NONBONDED TABLE SIZE: 769 POINTS > > Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 11.8295 > > Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 5.45773e-14 AT 11.9138 > > Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 8.47033e-22 AT 11.9138 > > Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.6856e-15 AT 11.9138 > > Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-32 AT 11.8295 > > Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138 > > Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-32 AT 11.9138 > > Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-15 AT 11.9138 > > Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295 > > Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138 > > Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138 > > Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138 > > Info: Entering startup phase 8 with 8712 kB of memory in use. > > > > > > > > Chris Harrison wrote: > >> Anna, > >> > >> Did this produce a coredump file and did you configure with > >> "--with-debug" or using whatever debug flags are appropriate for the > >> pg compiler? > >> > >> > >> Chris > >> > >> > >> -- > >> Chris Harrison, Ph.D. > >> Theoretical and Computational Biophysics Group > >> NIH Resource for Macromolecular Modeling and Bioinformatics > >> Beckman Institute for Advanced Science and Technology > >> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 > >> > >> char_at_ks.uiuc.edu <mailto:char_at_ks.uiuc.edu> > >> Voice: 217-244-1733 > >> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar> < > http://www.ks.uiuc.edu/%7Echar> > >> Fax: 217-244-6078 > >> > >> > >> > >> On Mon, Jun 15, 2009 at 3:49 AM, Anna Dejardin > >> <anna.dejardin_at_ucl.ac.uk <mailto:anna.dejardin_at_ucl.ac.uk>> wrote: > >> > >> Hi Peter, > >> > >> Thanks for your advice. I'm still having problems unfortunately. > >> We've tried recompiling with TCL 8.4 support. My compiler is > >> Portland Group 7.2-5 and my operating system is Redhat Enterprise > >> Linux 5. I'm still getting error messages when I try to run the > >> tutorial programs. Example: > >> > >> Error: in routine alloca() there is a > >> stack overflow: thread 0, max 10228KB, used 4KB, request -18888208B > >> > >> We are a bit stumped. Any ideas? > >> > >> Thanks so much > >> > >> Anna > >> > >> > >> Peter Freddolino wrote: > >> > >> Hi Anna, > >> it looks like your namd binary wasn't built with tcl support. > >> While you > >> can get namd to work this way, many features will be disabled, > >> and the > >> syntax in the tutorials assumes a fully functional build. I'd > >> recommend > >> either rebuilding with tcl support or using one of the > >> precompiled > >> binaries available on the namd website. > >> Best, > >> Peter > >> > >> Anna Dejardin wrote: > >> > >> Hi Peter, > >> > >> Here is the logfile: > >> > >> Charm++> Running on MPI version: 1.2 multi-thread support: > >> 1/0 > >> Charm warning> Randomization of stack pointer is turned on > >> in Kernel, > >> run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root > >> to disable > >> it. Thread migration may not work! > >> Info: NAMD 2.6 for Linux-amd64-MPI > >> Info: > >> Info: Please visit http://www.ks.uiuc.edu/Research/namd/ > >> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu > >> <mailto:namd_at_ks.uiuc.edu> > >> Info: > >> Info: Please cite Phillips et al., J. Comp. Chem. > >> 26:1781-1802 (2005) > >> Info: in all publications reporting results obtained with > >> NAMD. > >> Info: > >> Info: Based on Charm++/Converse 60000 for > >> mpi-linux-amd64-pgf90-mpicxx > >> Info: Built Tue May 5 12:36:23 BST 2009 by atg on > >> reinette.lcn.ucl.ac.uk <http://reinette.lcn.ucl.ac.uk> > >> Info: 1 NAMD 2.6 Linux-amd64-MPI 1 > >> reinette.lcn.ucl.ac.uk <http://reinette.lcn.ucl.ac.uk> acd > >> Info: Running on 1 processors. > >> Info: 1592 kB of memory in use. > >> Info: Memory usage based on mallinfo > >> Info: Changed directory to > >> /homes/acd/NAMD2.6/namd-tutorial-files/1-2-sphere > >> Info: Configuration file is ubq_ws_eq.conf > >> ERROR: Expecting value and optional units for option > >> 'temperature' > >> ERROR: Expecting value and optional units for option > >> 'langevinTemp' > >> ERROR: The following variables were set in the > >> ERROR: configuration file but are NOT VALID > >> ERROR: run > >> ERROR: reinitvels > >> ERROR: minimize > >> ERROR: set > >> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE > >> p0_14453: p4_error: : 1 > >> > >> Thanks > >> > >> Anna > >> ** > >> ** Visit http://www.greatcircle.com/majordomo/ for more > >> info on majordomo > >> ** > >> > >> ** > >> ** Visit http://www.greatcircle.com/majordomo/ for more info > >> on majordomo > >> ** > >> > >> > >> ** > >> ** Visit http://www.greatcircle.com/majordomo/ for more info on > >> majordomo > >> ** > >> > >> > ** ** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo **
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