User Codes

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Astrophysics

Athena (explicit, uniform grid MHD code)

Athena scaling on GPC with OpenMPI and MVAPICH2 on GigE, and OpenMPI on InfiniBand

Athena is a straightforward C code which doesn't use a lot of libraries so it is pretty straightforward to build and compile on new machines.

It encapsulates its compiler flags, etc in an Makeoptions.in file which is then processed by configure. I've used the following additions to Makeoptions.in on TCS and GPC:

<source lang="sh"> ifeq ($(MACHINE),scinettcs)

 CC = mpcc_r
 LDR = mpcc_r
 OPT = -O5 -q64 -qarch=pwr6 -qtune=pwr6 -qcache=auto -qlargepage -qstrict
 MPIINC =
 MPILIB =
 CFLAGS = $(OPT)
 LIB = -ldl -lm

else ifeq ($(MACHINE),scinetgpc)

 CC = mpicc
 LDR = mpicc
 OPT = -O3
 MPIINC =
 MPILIB =
 CFLAGS = $(OPT)
 LIB = -lm

else ... endif endif </source> It performs quite well on the GPC, scaling extremely well even on a strong scaling test out to about 256 cores (32 nodes) on Gigabit ethernet, and performing beautifully on InfiniBand out to 512 cores (64 nodes).


-- ljdursi 19:20, 13 August 2009 (UTC)

FLASH3 (Adaptive Mesh reactive hydrodynamics; explict hydro/MHD)

Weak scaling test of the 2d sod problem on both the GPC and TCS. The results are actually somewhat faster on the GPC; in both cases (weak) scaling is very good out at least to 256 cores

FLASH encapsulates its machine-dependant information in the FLASH3/sites directory. For the GPC, you'll have to

module load intel
module load openmpi
module load hdf5/183-v16-openmpi

and with that, the following file (sites/scinetgpc/Makefile.h) works for me: <source lang="sh">

    1. Must do module load hdf5/183-v16-openmpi

HDF5_PATH = ${SCINET_HDF5_BASE} ZLIB_PATH = /usr/local

  1. ----------------------------------------------------------------------------
  2. Compiler and linker commands
  3. We use the f90 compiler as the linker, so some C libraries may explicitly
  4. need to be added into the link line.
  5. ----------------------------------------------------------------------------
    1. modules will put the right mpi in our path

FCOMP = mpif77 CCOMP = mpicc CPPCOMP = mpiCC LINK = mpif77

  1. ----------------------------------------------------------------------------
  2. Compilation flags
  3. Three sets of compilation/linking flags are defined: one for optimized
  4. code, one for testing, and one for debugging. The default is to use the
  5. _OPT version. Specifying -debug to setup will pick the _DEBUG version,
  6. these should enable bounds checking. Specifying -test is used for
  7. flash_test, and is set for quick code generation, and (sometimes)
  8. profiling. The Makefile generated by setup will assign the generic token
  9. (ex. FFLAGS) to the proper set of flags (ex. FFLAGS_OPT).
  10. ----------------------------------------------------------------------------

FFLAGS_OPT = -c -r8 -i4 -O3 -xSSE4.2 FFLAGS_DEBUG = -c -g -r8 -i4 -O0 FFLAGS_TEST = -c -r8 -i4


  1. if we are using HDF5, we need to specify the path to the include files

CFLAGS_HDF5 = -I${HDF5_PATH}/include

CFLAGS_OPT = -c -O3 -xSSE4.2 CFLAGS_TEST = -c -O2 CFLAGS_DEBUG = -c -g

MDEFS =

.SUFFIXES: .o .c .f .F .h .fh .F90 .f90

  1. ----------------------------------------------------------------------------
  2. Linker flags
  3. There is a seperate version of the linker flags for each of the _OPT,
  4. _DEBUG, and _TEST cases.
  5. ----------------------------------------------------------------------------

LFLAGS_OPT = -o LFLAGS_TEST = -o LFLAGS_DEBUG = -g -o

MACHOBJ =


MV = mv -f AR = ar -r RM = rm -f CD = cd RL = ranlib ECHO = echo </source>


-- ljdursi 22:11, 13 August 2009 (UTC)

Aeronautics

Chemistry

GAMESS (US)

The GAMESS version January 12, 2009 R3 was built using the Intel v11.1 compilers and v3.2.2 MPI library, according to the instructions in http://software.intel.com/en-us/articles/building-gamess-with-intel-compilers-intel-mkl-and-intel-mpi-on-linux/

The required build scripts - comp, compall, lked - and run script - rungms - were modified to account for our own installation. In order to build GAMESS one first must ensure that the intel and intelmpi modules are loaded ("module load intel intelmpi"). This applies to running GAMESS as well. The module "gamess" must also be loaded in order to run GAMESS ("module load gamess").

The modified scripts are in the file /scinet/gpc/src/gamess-on-scinet.tar.gz

Running GAMESS

- Make sure the directory /scratch/$USER/gamess-scratch exists (the $SCINET_RUNGMS script will create it if it does not exist)

- Make sure the modules: intel, intelmpi, gamess are loaded (in your .bashrc: "module load intel intelmpi gamess").

- Create a torque script to run GAMESS. Here is an example:

- The GAMESS executable is in $SCINET_GAMESS_HOME/gamess.00.x - The rungms script is in $SCINET_GAMESS_HOME/rungms (actually it is $SCINET_RUNGMS)

- For IB multinode runs, use the $SCINET_RUNGMS_IB script

- The rungms script takes 4 arguments: input file, executable number, number of compute processes, processors per node

For example, in order to run with the input file /scratch/$USER/gamesstest01, on 8 cpus, and the default version (00) of the executable on a machine with 8 cores:

  # load the gamess module in .bashrc
  module load gamess  
  # run the program
  $SCINET_RUNGMS /scratch/$USER/gamesstest01 00 8 8

Here is a sample torque script for running a GAMESS calculation, on a single 8-core node:

<source lang="bash">

  1. !/bin/bash
  2. PBS -l nodes=1:ppn=8,walltime=48:00:00,os=centos53computeA
  3. PBS -N gamessjob
    1. To submit type: qsub gms.sh
  1. If not an interactive job (i.e. -I), then cd into the directory where
  2. I typed qsub.

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then

  if [ -n "$PBS_O_WORKDIR" ]; then
    cd $PBS_O_WORKDIR
  fi

fi

  1. the input file is typically named something like "gamesjob.inp"
  2. so the script will be run like "$SCINET_RUNGMS gamessjob 00 8 8"
  1. load the gamess module if not in .bashrc already
  2. actually, it MUST be in .bashrc
  3. module load gamess
  1. run the program

$SCINET_RUNGMS gamessjob 00 8 8 </source>

Here is a similar script, but this one uses 2 InfiniBand-connected nodes, and runs the appropriate $SCINET_RUNGMS_IB script to actually run the job:

<source lang="bash">

  1. !/bin/bash
  2. PBS -l nodes=2:ib:ppn=8,walltime=48:00:00,os=centos53computeA
  3. PBS -N gamessjob
    1. To submit type: qsub gmsib.sh
  1. If not an interactive job (i.e. -I), then cd into the directory where
  2. I typed qsub.

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then

  if [ -n "$PBS_O_WORKDIR" ]; then
    cd $PBS_O_WORKDIR
  fi

fi

  1. the input file is typically named something like "gamesjob.inp"
  2. so the script will be run like "$SCINET_RUNGMS gamessjob 00 8 8"
  1. load the gamess module if not in .bashrc already
  2. actually, it MUST be in .bashrc
  3. module load gamess
  1. This script requests InfiniBand-connected nodes (:ib above)
  2. so it must run with the IB version of the rungms script,
  3. $SCINET_RUNGMS_IB

$SCINET_RUNGMS_IB gamessjob 00 16 8 </source>


-- dgruner 5 October 2009

Tips from the Fekl Lab

Through trial and error, we have found a few useful things that we would like to share:

1. Two very useful, open-source programs for visualization of output files from GAMESS(US) and for generation of input files are MacMolPltand Avogadro. The are available for UNIX/LINUX, Windows and Mac based machines, HOWEVER: any input files that we have generated with these programs on a Windows-based machine do not run on Mac based machines. We don't know why.

2. WinSCP is a very useful tool that has a graphical user interface for moving files from a local machine to SCINET and vice versa. It also has text editing capabilities.

3. The ESML Basis Set Exchange is an excellent source for custom basis set or effective core potential parameters. Make sure that you specify "Gamess-US" in the format drop-down box.

4. The commercial program ChemCraft is a highly useful visualization program that has the ability to edit molecules in a very similar fashion to GaussView. It can also be customized to build GAMESS(US) input files.

Anatomy of a GAMESS(US) Input File with Basis Set Info in an External File

 $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE DFTTYP=M06-L MAXIT=199 MULT=1 NOSYM=1
  ECP=READ $END
 $SYSTEM TIMLIM=525600 MWORDS=1750 PARALL=.TRUE. $END
 $BASIS GBASIS=CUSTOMNI EXTFIL=.t. $END
 $SCF DIRSCF=.TRUE. FDIFF=.f. $END
 $STATPT OPTTOL=0.0001 NSTEP=500 HSSEND=.t. $END
 $DATA
 Mo_BDT3
C1
MOLYBDENUM 42.0      5.7556500000      4.4039600000     16.5808400000
SULFUR     16.0      7.4169700000      3.1956300000     15.2089300000
SULFUR     16.0      4.0966800000      3.2258300000     15.1761100000
SULFUR     16.0      3.9677300000      4.4940500000     18.3266100000
SULFUR     16.0      7.1776900000      3.5815000000     18.4485200000
SULFUR     16.0      4.3776600000      6.2447400000     15.6786900000
SULFUR     16.0      7.5478700000      6.0679800000     16.2223700000
CARBON      6.0      6.4716900000      2.1004800000     14.1902300000
CARBON      6.0      5.0690300000      2.1781400000     14.1080700000
CARBON      6.0      4.8421800000      4.2701300000     19.8855500000
CARBON      6.0      6.1969000000      3.9249600000     19.9397400000
CARBON      6.0      6.8280600000      3.7834200000     21.1913200000
CARBON      6.0      5.7697600000      7.6933500000     17.4241800000
CARBON      6.0      7.2043100000      7.9413600000     17.8281100000
CARBON      6.0      5.5051400000      7.0409700000     14.5903800000
CARBON      6.0      6.8905200000      6.9194700000     14.7626200000
CARBON      6.0      7.7396400000      7.5379800000     13.8285700000
HYDROGEN    1.0      8.8190700000      7.4520600000     13.9252200000
CARBON      6.0      7.2169400000      8.2960300000     12.7704100000
HYDROGEN    1.0      7.8667000000      8.7825100000     12.0575600000
CARBON      6.0      5.8260300000      8.4502300000     12.6467800000
HYDROGEN    1.0      5.4143000000      9.0544300000     11.8493100000
CARBON      6.0      4.9881500000      7.8192300000     13.5528400000
HYDROGEN    1.0      3.9090500000      7.9420000000     13.4583700000
CARBON      6.0      7.1538500000      1.1569600000     13.4143900000
CARBON      6.0      4.4018100000      1.3603900000     13.1919900000
CARBON      6.0      6.4791600000      0.3185500000     12.5353300000
CARBON      6.0      5.0837400000      0.4369500000     12.4084900000
HYDROGEN    1.0      7.0116000000     -0.4099400000     11.9434600000
HYDROGEN    1.0      8.2399000000      1.0702400000     13.4937600000
HYDROGEN    1.0      3.3185600000      1.4368700000     13.0953100000
HYDROGEN    1.0      4.5549800000     -0.1997300000     11.7165200000
CARBON      6.0      6.1105700000      3.9639000000     22.3866100000
CARBON      6.0      4.1216300000      4.4424400000     21.1020100000
HYDROGEN    1.0      7.8732900000      3.5217100000     21.2520500000
CARBON      6.0      4.7606000000      4.2868500000     22.3363800000
HYDROGEN    1.0      6.6064200000      3.8406000000     23.3428500000
HYDROGEN    1.0      4.2065000000      4.4170700000     23.2667100000
HYDROGEN    1.0      3.0674000000      4.6893500000     21.0889000000
HYDROGEN    1.0      7.4249200000      7.7545300000     18.8583200000
HYDROGEN    1.0      7.6651700000      8.9049700000     17.7652100000
HYDROGEN    1.0      5.3324000000      8.6487800000     17.2222700000
HYDROGEN    1.0      5.5015000000      7.1039000000     18.2759400000
 $END
 $ECP
MO-ECP GEN     28     3
 5      ----- f potential     -----
    -0.0469492        0    537.9667807        
   -20.2080084        1    147.8982938        
  -106.2116302        2     45.7358898        
   -41.8107368        2     13.2911467        
    -4.2054103        2      4.7059961        
 3      ----- s-f potential     -----
     2.8063717        0    110.2991760        
    44.5162012        1     23.2014645        
    82.7785227        2      5.3530131        
 4      ----- p-f potential     -----
     4.9420876        0     63.2901397        
    25.8604976        1     23.3315302        
   132.4708742        2     24.6759423        
    57.3149794        2      4.6493040        
 5      ----- d-f potential     -----
     3.0054591        0    104.4839977        
    26.3637851        1     66.2307245        
   183.3849199        2     39.1283176        
    98.4453068        2     13.1164437        
    22.4901377        2      3.6280263 
S NONE
S NONE
S NONE
S NONE
S NONE
S NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
H NONE
C NONE
H NONE
C NONE
H NONE
C NONE
H NONE
C NONE
C NONE
C NONE
C NONE
H NONE
H NONE
H NONE
H NONE
C NONE
C NONE
H NONE
C NONE
H NONE
H NONE
H NONE
H NONE
H NONE
H NONE
H NONE
 $END
The Input Deck

This is the input deck. It is where you tell GAMESS(US) what job type to execute and where all you individual parameters are entered for your specific job type. The example input deck below is for a geometry optimization and frequency calculation. This input deck is equivalent to the Gaussian job with "opt" and "freq" in the route section.

 $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE DFTTYP=M06-L MAXIT=199 MULT=1 NOSYM=1
  ECP=READ $END
 $SYSTEM TIMLIM=525600 MWORDS=1750 PARALL=.TRUE. $END
 $BASIS GBASIS=CUSTOMNI EXTFIL=.t. $END
 $SCF DIRSCF=.TRUE. FDIFF=.f. $END
 $STATPT OPTTOL=0.0001 NSTEP=500 HSSEND=.t. $END
 $DATA

An important thing to note is the spacing. In the input deck, there must be 1 space at the beginning of each line of the input deck. If not, the job will fail. Most builders will insert this space anyway, but it help to double check.

The end of the input deck is marked by the "$DATA" line.

Job Title Line

The next line of the file is the job title. It can be anthing you wish, however, we have found that to be on the safe side, we avoide using symbols or spaces

 Mo_BDT3
Symmetry Point Group

The next line of the file is the symmetry point group of your molecule. Note that there is no leading space before the point group.

C1
Coordinates

The next block of text is set aside for the coordinates of the molecule. This can be in internal (or z-matrix) format or cartesian coordinates. Note that there is no leading space before the coordinates. One may use the chemical symbol or the full name of each atom in the molecule. Note that the end of the coordinates is signified by an "$END", which MUST have one space preceding it.

MOLYBDENUM 42.0      5.7556500000      4.4039600000     16.5808400000
SULFUR     16.0      7.4169700000      3.1956300000     15.2089300000
SULFUR     16.0      4.0966800000      3.2258300000     15.1761100000
SULFUR     16.0      3.9677300000      4.4940500000     18.3266100000
SULFUR     16.0      7.1776900000      3.5815000000     18.4485200000
SULFUR     16.0      4.3776600000      6.2447400000     15.6786900000
SULFUR     16.0      7.5478700000      6.0679800000     16.2223700000
CARBON      6.0      6.4716900000      2.1004800000     14.1902300000
CARBON      6.0      5.0690300000      2.1781400000     14.1080700000
CARBON      6.0      4.8421800000      4.2701300000     19.8855500000
CARBON      6.0      6.1969000000      3.9249600000     19.9397400000
CARBON      6.0      6.8280600000      3.7834200000     21.1913200000
CARBON      6.0      5.7697600000      7.6933500000     17.4241800000
CARBON      6.0      7.2043100000      7.9413600000     17.8281100000
CARBON      6.0      5.5051400000      7.0409700000     14.5903800000
CARBON      6.0      6.8905200000      6.9194700000     14.7626200000
CARBON      6.0      7.7396400000      7.5379800000     13.8285700000
HYDROGEN    1.0      8.8190700000      7.4520600000     13.9252200000
CARBON      6.0      7.2169400000      8.2960300000     12.7704100000
HYDROGEN    1.0      7.8667000000      8.7825100000     12.0575600000
CARBON      6.0      5.8260300000      8.4502300000     12.6467800000
HYDROGEN    1.0      5.4143000000      9.0544300000     11.8493100000
CARBON      6.0      4.9881500000      7.8192300000     13.5528400000
HYDROGEN    1.0      3.9090500000      7.9420000000     13.4583700000
CARBON      6.0      7.1538500000      1.1569600000     13.4143900000
CARBON      6.0      4.4018100000      1.3603900000     13.1919900000
CARBON      6.0      6.4791600000      0.3185500000     12.5353300000
CARBON      6.0      5.0837400000      0.4369500000     12.4084900000
HYDROGEN    1.0      7.0116000000     -0.4099400000     11.9434600000
HYDROGEN    1.0      8.2399000000      1.0702400000     13.4937600000
HYDROGEN    1.0      3.3185600000      1.4368700000     13.0953100000
HYDROGEN    1.0      4.5549800000     -0.1997300000     11.7165200000
CARBON      6.0      6.1105700000      3.9639000000     22.3866100000
CARBON      6.0      4.1216300000      4.4424400000     21.1020100000
HYDROGEN    1.0      7.8732900000      3.5217100000     21.2520500000
CARBON      6.0      4.7606000000      4.2868500000     22.3363800000
HYDROGEN    1.0      6.6064200000      3.8406000000     23.3428500000
HYDROGEN    1.0      4.2065000000      4.4170700000     23.2667100000
HYDROGEN    1.0      3.0674000000      4.6893500000     21.0889000000
HYDROGEN    1.0      7.4249200000      7.7545300000     18.8583200000
HYDROGEN    1.0      7.6651700000      8.9049700000     17.7652100000
HYDROGEN    1.0      5.3324000000      8.6487800000     17.2222700000
HYDROGEN    1.0      5.5015000000      7.1039000000     18.2759400000
 $END
Effective Core Potential Data

The effective core potential (ECP) data is entered after the coordinates. It starts with "$ECP", which must be preceded with a space. The atoms of the molecule are listed in the same order as in the coordinates section and the parameters for the ECP are listed after each atom. Note that for any atom that does NOT have an ECP, one must enter "ECP-NONE" or "NONE" after each atom without an ECP.

$ECP
MO-ECP GEN     28     3
 5      ----- f potential     -----
    -0.0469492        0    537.9667807        
   -20.2080084        1    147.8982938        
  -106.2116302        2     45.7358898        
   -41.8107368        2     13.2911467        
    -4.2054103        2      4.7059961        
 3      ----- s-f potential     -----
     2.8063717        0    110.2991760        
    44.5162012        1     23.2014645        
    82.7785227        2      5.3530131        
 4      ----- p-f potential     -----
     4.9420876        0     63.2901397        
    25.8604976        1     23.3315302        
   132.4708742        2     24.6759423        
    57.3149794        2      4.6493040        
 5      ----- d-f potential     -----
     3.0054591        0    104.4839977        
    26.3637851        1     66.2307245        
   183.3849199        2     39.1283176        
    98.4453068        2     13.1164437        
    22.4901377        2      3.6280263 
S NONE
S NONE
S NONE
S NONE
S NONE
S NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
C NONE
H NONE
C NONE
H NONE
C NONE
H NONE
C NONE
H NONE
C NONE
C NONE
C NONE
C NONE
H NONE
H NONE
H NONE
H NONE
C NONE
C NONE
H NONE
C NONE
H NONE
H NONE
H NONE
H NONE
H NONE
H NONE
H NONE
 $END

-- mzd 16 November 2009

Using Effective Core Potentials in GAMESS(US)

For many metal containing compounds, it is very convenient and time saving to use an effective core potential (ECP) for the core metal electrons, as they are usually not important to the reactivity of the complex or the geometry around the metal. Since GAMESS(US) has a limited number of built-in ECPs, one may want to make GAMESS(US) read an external file that contains the ECP data using the "EXTFIL" keyword in the $GBASIS command line of the input file. In addition, to make GAMESS(US) use this external file, one must copy the "rungms" file and modify it accordingly. The following is a list of instructions with commands that will work from a terminal. One could also use WinSCP to do all of this with a GUI rather than a TUI.

Modifiying rungms to Use Custom Basis Set File

1. Copy "rungms" from /scinet/gpc/Applications/gamess to one's own /scratch/$USER/ directory:

cp /scinet/gpc/Applications/gamess/rungms /scratch/$USER/

2. Change to the scratch directory and check to see if "rungms" has copied successfully.

cd /scratch/$USER
ls

3. Edit line 147 of the vi.

vi rungms

Move the cursor down to line 147 using the arrow keys. It should say "setenv EXTBAS /dev/null". Using the arrow keys, move the cursor to the first "/" and then hit "i" to insert text. Put the path to your external basis file here. For example, /scratch/$USER/basisset. Then hit "escape". To save the changes and exit vi, type ":" and you should see a colon appear at the bottom of the window. Type "wq" (which should appear at the bottom of the window next to the colon) and then hit enter. Now you are done with vi.

Creating a Custom Basis Set File

1. To create a custom basis set file, you need create a new text document. Our group's common practice is to comment out the first line of this file by inserting an exclamation mark (!) followed by noting the specific basis sets and ECPs that are going to be used for each of the atoms. Let us the molecule Mo(CO)6, Molybdenum hexacarbonyl, as an example. Below is the first line of the the external file, which we will call "CUSTOMMO" (NOTE: you can use any name for the external file that suits you, as long as it has no spaces and is 8 characters or less).

! 6-31G on C and O and LANL2D2 ECP on Mo

2. The next step is to visit the EMSL Basis Set exchange and select C and O from the periodic table. Then, on the left of the page, select "6-31G" as the basis set. Finally, make sure the output is in GAMESS(US) format using the drop-down menu and then click "get basis set".

C O 6 31G basisset.JPG

3. A new window should appear with text in it. For our example case, the text looks like this:

!  6-31G  EMSL  Basis Set Exchange Library   10/13/09 11:12 AM
! Elements                             References
! --------                             ----------
! H - He: W.J. Hehre, R. Ditchfield and J.A. Pople, J. Chem. Phys. 56,
! Li - Ne: 2257 (1972).  Note: Li and B come from J.D. Dill and J.A.
! Pople, J. Chem. Phys. 62, 2921 (1975).
! Na - Ar: M.M. Francl, W.J. Petro, W.J. Hehre, J.S. Binkley, M.S. Gordon,
! D.J. DeFrees and J.A. Pople, J. Chem. Phys. 77, 3654 (1982)
! K  - Zn: V. Rassolov, J.A. Pople, M. Ratner and T.L. Windus, J. Chem. Phys.
! 109, 1223 (1998)
! Note: He and Ne are unpublished basis sets taken from the Gaussian
! program
! 
$DATA
CARBON S 6 1 3047.5249000 0.0018347 2 457.3695100 0.0140373 3 103.9486900 0.0688426 4 29.2101550 0.2321844 5 9.2866630 0.4679413 6 3.1639270 0.3623120 L 3 1 7.8682724 -0.1193324 0.0689991 2 1.8812885 -0.1608542 0.3164240 3 0.5442493 1.1434564 0.7443083 L 1 1 0.1687144 1.0000000 1.0000000
OXYGEN S 6 1 5484.6717000 0.0018311 2 825.2349500 0.0139501 3 188.0469600 0.0684451 4 52.9645000 0.2327143 5 16.8975700 0.4701930 6 5.7996353 0.3585209 L 3 1 15.5396160 -0.1107775 0.0708743 2 3.5999336 -0.1480263 0.3397528 3 1.0137618 1.1307670 0.7271586 L 1 1 0.2700058 1.0000000 1.0000000 $END

3. Now, copy and paste the text between the $DATA and $END headings onto our external text file, CUSTOMMO. We also need to change the change the name of each element to it symbol in the periodic table. Finally, we need to add the name of the external file next to the element symbol, separated by one space. Note that there should be a blank line separating the basis set information and the first, commented-out line (The line starting with the '!'). The CUSTOMMO should look like this:

! 6-31G on C and O and LANL2D2 ECP on Mo
C CUSTOMMO S 6 1 3047.5249000 0.0018347 2 457.3695100 0.0140373 3 103.9486900 0.0688426 4 29.2101550 0.2321844 5 9.2866630 0.4679413 6 3.1639270 0.3623120 L 3 1 7.8682724 -0.1193324 0.0689991 2 1.8812885 -0.1608542 0.3164240 3 0.5442493 1.1434564 0.7443083 L 1 1 0.1687144 1.0000000 1.0000000
O CUSTOMMO S 6 1 5484.6717000 0.0018311 2 825.2349500 0.0139501 3 188.0469600 0.0684451 4 52.9645000 0.2327143 5 16.8975700 0.4701930 6 5.7996353 0.3585209 L 3 1 15.5396160 -0.1107775 0.0708743 2 3.5999336 -0.1480263 0.3397528 3 1.0137618 1.1307670 0.7271586 L 1 1 0.2700058 1.0000000 1.0000000

4. Repeat Step 3 above but choose Mo and select the LANL2DZ ECP instead. A new window will pop up with the basis set information as well as the ECP data we need, since we specified the LANL2DZ ECP. The ECP data is not inserted into the external file, rather it is placed into the input file itself (More on this later).

Mo LANL2DZ basisset.JPG

5. After copying the molybdenum basis set information, your fiished external basis set file should look like this:

! 6-31G on C and O and LANL2D2 ECP on Mo
C CUSTOMMO S 6 1 3047.5249000 0.0018347 2 457.3695100 0.0140373 3 103.9486900 0.0688426 4 29.2101550 0.2321844 5 9.2866630 0.4679413 6 3.1639270 0.3623120 L 3 1 7.8682724 -0.1193324 0.0689991 2 1.8812885 -0.1608542 0.3164240 3 0.5442493 1.1434564 0.7443083 L 1 1 0.1687144 1.0000000 1.0000000
O CUSTOMMO S 6 1 5484.6717000 0.0018311 2 825.2349500 0.0139501 3 188.0469600 0.0684451 4 52.9645000 0.2327143 5 16.8975700 0.4701930 6 5.7996353 0.3585209 L 3 1 15.5396160 -0.1107775 0.0708743 2 3.5999336 -0.1480263 0.3397528 3 1.0137618 1.1307670 0.7271586 L 1 1 0.2700058 1.0000000 1.0000000
Mo CUSTOMO S 3 1 2.3610000 -0.9121760 2 1.3090000 1.1477453 3 0.4500000 0.6097109 S 4 1 2.3610000 0.8139259 2 1.3090000 -1.1360084 3 0.4500000 -1.1611592 4 0.1681000 1.0064786 S 1 1 0.0423000 1.0000000 P 3 1 4.8950000 -0.0908258 2 1.0440000 0.7042899 3 0.3877000 0.3973179 P 2 1 0.4995000 -0.1081945 2 0.0780000 1.0368093 P 1 1 0.0247000 1.0000000 D 3 1 2.9930000 0.0527063 2 1.0630000 0.5003907 3 0.3721000 0.5794024 D 1 1 0.1178000 1.0000000

-- mzd 13 October 2009

Climate Modelling

Medicine/Bio

High Energy Physics

Structural Biology

Molecular simulation of proteins, lipids, carbohydrates, and other biologically relevant molecules.

Molecular Dynamics (MD) simulation

GROMACS

Please refer to the GROMACS page

NAMD

NAMD is one of the better scaling MD packages out there. With sufficiently large systems, it is able to scale to hundreds or thousands of cores on Scinet. Below are details for compiling and running NAMD on Scinet.

More information regarding performance and different compile options coming soon...

Compiling NAMD for GPC

Ensure the proper compiler/mpi modules are loaded. <source lang="sh"> module load intel module load openmpi/1.3.3-intel-v11.0-ofed </source>

Compile Charm++ and NAMD <source lang="sh">

  1. Unpack source files and get required support libraries

tar -xzf NAMD_2.7b1_Source.tar.gz cd NAMD_2.7b1_Source tar -xf charm-6.1.tar wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl-linux-x86_64.tar.gz tar -xzf fftw-linux-x86_64.tar.gz; mv linux-x86_64 fftw tar -xzf tcl-linux-x86_64.tar.gz; mv linux-x86_64 tcl

  1. Compile Charm++

cd charm-6.1 ./build charm++ mpi-linux-x86_64 icc --basedir /scinet/gpc/mpi/openmpi/1.3.3-intel-v11.0-ofed/ --no-shared -O -DCMK_OPTIMIZE=1 cd ..

  1. Compile NAMD.
  2. Edit arch/Linux-x86_64-icc.arch and add "-lmpi" to the end of the CXXOPTS and COPTS line.
  3. Make a builds directory if you want different versions of NAMD compiled at the same time.

mkdir builds ./config builds/Linux-x86_64-icc --charm-arch mpi-linux-x86_64-icc cd builds/Linux-x86_64-icc/ make -j4 namd2 # Adjust value of j as desired to specify number of simultaneous make targets. </source> --Cmadill 16:18, 27 August 2009 (UTC)

Running Fortran

On the development nodes, there is an old gcc. The associated libraries are not on the compute nodes. Ensure the line:

module load gcc

is in your .bashrc file.


Monte Carlo (MC) simulation