INSTALLING GAMESS in Hemanadhan's Computer @ FB 483

1. Download "gamess-current.tar.Z" to directory (say '/home/hemanadh') 2. Open terminal and cd to "gamess-current.tar.Z" directory cd/home/hemanadh 3. Unzip/Gunzip the file. tarxzvf/home/hemanadh/gamesscurrent.tar.gz or zcatgamesscurrent.tar.Z|tarxvf This creats a directory "gamess" 4. Change to gamess directory cdgamess 5. Read vimmisc/readme.unix 6. Type ./config This script asks a few questions, depending on your computer system, to set up compiler names, libraries, message passing libraries, and so forth. You can quit at any time by pressing control-C, and then <return>. PressEnter

Please open a second window by logging into your target machine, in case this script asks you to 'type' a command to learn something about your system software situation. All such extra questions will use the word 'type' to indicate it is a command for the other window. After the new window is open, please hit <return> to go on. GAMESS can compile on the following 32 bit or 64 bit machines: axp64 - Alpha chip, native compiler, running Tru64 or Linux cray-xt - Cray's massively parallel system, running CNL hpux32 - HP PA-RISC chips (old models only), running HP-UX hpux64 - HP Intel or PA-RISC chips, running HP-UX ibm32 - IBM (old models only), running AIX ibm64 - IBM, Power3 chip or newer, running AIX or Linux ibm64-sp - IBM SP parallel system, running AIX ibm-bg - IBM Blue Gene (P or L model), these are 32 bit systems linux32 - Linux (any 32 bit distribution), for x86 (old systems only) linux64 - Linux (any 64 bit distribution), for x86_64 or ia64 chips AMD/Intel chip Linux machines are sold by many companies mac32 - Apple Mac, any chip, running OS X 10.4 or older mac64 - Apple Mac, any chip, running OS X 10.5 or newer sgi32 - Silicon Graphics Inc., MIPS chip only, running Irix sgi64 - Silicon Graphics Inc., MIPS chip only, running Irix sun32 - Sun ultraSPARC chips (old models only), running Solaris sun64 - Sun ultraSPARC or Opteron chips, running Solaris win32 - Windows 32-bit (Windows XP, Vista, 7, Compute Cluster, HPC Edition)

win64 - Windows 64-bit (Windows XP, Vista, 7, Compute Cluster, HPC Edition) type 'uname -a' to partially clarify your computer's flavor. please enter your target machine name: linux64 PressEnter {If you dont know Open a new terminal and type 'uname -a' ==> 'Linux Hemanadhan 2.6.31-22-generic #70-Ubuntu SMP Wed Dec 1 23:48:17 UTC 2010 x86_64 GNU/Linux ' } Where is the GAMESS software on your system? A typical response might be /u1/mike/gamess, most probably the correct answer is /home/hemanadh/gamess GAMESS directory? [/home/hemanadh/gamess] PressEnter

Setting up GAMESS compile and link for GMS_TARGET=linux64 GAMESS software is located at GMS_PATH=/home/hemanadh/gamess Linux offers many choices for FORTRAN compilers, including the GNU compiler set ('g77' in old versions of Linux, or 'gfortran' in current versions), which are included for free in Unix distributions. There are also commercial compilers, namely Intel's 'ifort', Portland Group's 'pgf77', and Pathscale's 'pathf90'. The last two are not common, and aren't as well tested as the others. type 'rpm -aq | grep gcc' to check on all GNU compilers, including gcc type 'which gfortran' to look for GNU's gfortran (a very good choice), type 'which g77' to look for GNU's g77, type 'which ifort' to look for Intel's compiler, type 'which pgf77' to look for Portland Group's compiler, type 'which pathf90' to look for Pathscale's compiler. Please enter your choice of FORTRAN: gfortran gfortran is very robust, so this is a wise choice. gfortran does not support quadruple precision, so heavy element DK3 resolution of the identity will fail but everything else will work. hit <return> to continue to the math library setup. PressEnter

Linux distributions do not include a standard math library. There are several reasonable add-on library choices, MKL from Intel for 32 or 64 bit Linux (very fast) ACML from AMD for 32 or 64 bit Linux (free) ATLAS from www.rpmfind.net for 32 or 64 bit Linux (free) and one very unreasonable option, namely 'none', which will use some slow FORTRAN routines supplied with GAMESS. Choosing 'none' will run MP2 jobs 2x slower, or CCSD(T) jobs 5x slower. Some typical places (but not the only ones) to find math libraries are Type 'ls /opt/intel/mkl' to look for MKL Type 'ls /opt/intel/Compiler' to look for MKL Type 'ls -d /opt/acml*' to look for ACML Type 'ls /usr/lib64/atlas' to look for Atlas Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none': Math library 'none' will be taken from none

please hit <return> to compile the GAMESS source code activator PressEnter gfortran -o tools/actvte.x actvte.f unset echo Source code activator was successfully compiled. please hit <return> to set up your network for Linux clusters. If you have a slow network, like Gigabit Ethernet (GE), or if you have so few nodes you won't run extensively in parallel, or if you have no MPI library installed, or if you want a fail-safe compile/link and easy execution, choose 'sockets' to use good old reliable standard TCP/IP networking. If you have an expensive but fast network like Infiniband (IB), and if you have an MPI library correctly installed, choose 'mpi'. communication library ('sockets' or 'mpi')? Your configuration for GAMESS compilation is now in install.info Please follow the directions in /home/hemanadh/gamess/misc/readme.unix... sockets PressEnter

07. Login in as root

su

08. Type /sbin/sysctlwkernel.shmmax=1073741824 ==> Ref. Point 5 in readme. ==> To know "/sbin/sysctl -a | grep shm" ==> kernel.shmmax = 1610612736 kernel.shmall = 2097152 kernel.shmmni = 4096 09. Logout from root 10. Type 11. Type 12. Type 13. Change to GAMESS directory exit cdddi ./compddi>&compddi.log mvddikick.x.. cd..

14. Type ./compall>&compall.log {This command will take 30-60 minutes to execute} 15. Type ./lkedgamess00>&lked.log

16. Check whether the file 'gamess.00.x' is created. dir {This is the gamess executable} 17.Open the file rungms. Editthefollowinglines Line No. 58 Line No. 59 Line No. 60 Line No. 127 Line No. 128 Line No. 132 Line No. 133 Line No. 134 Line No. 135 Line No. 136 Line No. 137 Line No. 479 vimrungms setSCR=./ setUSERSCR=./ setGMSPATH=./ setenvERICFMT./ericfmt.dat setenvMCPPATH./mcpdata setenvMAKEFP$USERSCR/$JOB.efp setenvGAMMA$USERSCR/$JOB.gamma setenvTRAJECT$USERSCR/$JOB.trj setenvRESTART$USERSCR/$JOB.rst setenvINPUT$SCR/$JOB.F05 setenvPUNCH$USERSCR/$JOB.dat if($os==Linux)setGMSPATH=./

Commentthefollowinglines Line No. 521 #if($NCPUS==1)then Line No. 522 #setNNODES=1 Line No. 523 #setHOSTLIST=(`hostname`) Line No. 524 #endif Addthefollowinglines Line No. 525 Line No. 526 setHOSTLIST=(`hostname`:cpus=$NCPUS) setNNODES=1

Commentthefollowinglines Line No. 557 #echoIdonotknowhow torunthisnodeinparallel. Line No. 558 #exit20 SaveandQuit:wq 18. Open the file rungms. vimrunall

Commentthefollowinglines Line No. 13 #chdir/u1/mike/gamess SaveandQuit:wq 19. Type ./runall>&runall.log {Thiscommandwilltake1020mintoexecute} 20. Change directory to tools/checktst cdtools/checktst/ 22. Open the file vimchecktst

Editthefollowingline LineNo.9setGMSPATH=/home/hemanadh/gamess 23. Type ./checktst Please type the full directory containing exam??.log[.]: /home/hemanadh/gamess Checking the results of your sample GAMESS calculations, the output files (exam??.log) will be taken from /home/hemanadh/gamess All jobs terminated normally, now checking detailed numerical results exam01: Eerr=0.0e+00 Gerr=0.0e+00. exam02: Eerr=0.0e+00 Gerr=0.0e+00 Serr=0.0e+00 Lerr=1.8e-03+6.6e-05. exam03: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam04: Eerr=0.0e+00 Gerr=0.0e+00 Oerr=0.0e+00 Derr=0.0e+00. exam05: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam06: Eerr=0.0e+00 Gerr=0.0e+00.

Passed. Passed. Passed. Passed. Passed. Passed.

exam07: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam08: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam09: Eerr=8.0e-10. exam10: Eerr=0.0e+00 Werr=0.0e+00 Ierr=0.0e+00 Perr=0.0e+00. exam11: Eerr=0.0e+00 Rerr=0.0e+00. exam12: Eerr=0.0e+00 Gerr=0.0e+00. exam13: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam14: Eerr=0.0e+00+0.0e+00 Derr=0.0e+00+0.0e+00. exam15: Eerr=0.0e+00. exam16: Eerr=0.0e+00. exam17: Eerr=0.0e+00 Werr=0.0e+00 Ierr=0.0e+00 Perr=0.0e+00. exam18: Eerr=0.0e+00 Werr=0.0e+00. exam19: Eerr=0.0e+00+0.0e+00. exam20: Eerr=0.0e+00 Xerr=0.0e+00. exam21: Eerr=0.0e+00 Werr=0.0e+00 Ierr=0.0e+00 Perr=0.0e+00. exam22: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam23: Herr=0.0e+00 Gerr=0.0e+00. exam24: Eerr=0.0e+00 Gerr=0.0e+00 Derr=0.0e+00. exam25: Eerr=0.0e+00 Gerr=0.0e+00. exam26: Eerr=0.0e+00 Lerr=1.1e-07. exam27: Eerr=0.0e+00 Verr=0.0e+00. exam28: Eerr=0.0e+00. exam29: Eerr=0.0e+00. exam30: Eerr=0.0e+00 Gerr=0.0e+00. exam31: Eerr=0.0e+00 Gerr=0.0e+00 Ierr=0.0e+00. exam32: Eerr=4.9e-06 Terr=0.0e+00. exam33: Eerr=0.0e+00 Gerr=0.0e+00. exam34: Eerr=0.0e+00 Gerr=0.0e+00. exam35: Eerr=3.0e-08. exam36: Eerr=0.0e+00 Werr=0.0e+00 Ierr=0.0e+00. exam37: Eerr=0.0e+00 Gerr=0.0e+00. exam38: Eerr=7.0e-10 Gerr=0.0e+00. exam39: RIerr=0.0e+00 HRIerr=0.0e+00. exam40: E1err=0.0e+00 E2err=0.0e+00 RMSerr=0.0e+00 exam41: EXCerr=0.0e+00 eV, Gerr=0.0e+00, OSCerr=0.0e+00. exam42: Eerr=0.0e+00 Gerr=0.0e+00. exam43: HEATerr=0.0e+00 kcal/mol. exam44: SCFerr=0.0e+00 MP2err=0.0e+00. 1 job(s) got incorrect numerical results. Please examine why.

Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. !!FAILED. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed.

Note: Using MKL library will resolve the problem for 'exam32' or Check point 8 /sbin/sysctlwkernel.shmmax=1073741824

24. Change to GAMESS directory 25. Remove the compiled files 26. To run a GAMESS job 27. To view the output

cd../.. rmexam* ./rungmsexam01>&exam01.log vimexam01.log

28. Manual can be searched online by means of the gmshelp command cdtools vimgmshelp Editthefollowingline LineNo.19setdoc=/home/hemanadh/gamess/INPUT.DOC Type./tools/gmshelp

Ref. : ** Most of the about details can be found from the following website http://molecularmodelingbasics.blogspot.com/2010/08/compiling-gamess-on-linuxpc.html ** GAMESS Homepage http://www.msg.chem.iastate.edu/gamess/

ENJOY GAMESS
Hemanadhan Research Scholar

Color Code : Author Comments Instructionstobetyped Terminal Output

-------- Black -------- Brown ------- Green