tag:blogger.com,1999:blog-6701417360427959244.post1943710389461357352..comments2024-03-27T07:18:00.323+01:00Comments on Molecular Modeling Basics: Installing GAMESS on a linux PCJan Jensenhttp://www.blogger.com/profile/08595894308946022740noreply@blogger.comBlogger24125tag:blogger.com,1999:blog-6701417360427959244.post-35202761138380640432019-09-19T12:12:21.170+02:002019-09-19T12:12:21.170+02:00Hello.
Command - sudo /usr/local/gamess/rungms ex...Hello.<br />Command - sudo /usr/local/gamess/rungms exam01.inp<br /><br />LOG - <br />----- GAMESS execution script 'rungms' -----<br />This job is running on host work<br />under operating system Linux at Thu Sep 19 10:09:57 UTC 2019<br />Available scratch disk space (Kbyte units) at beginning of the job is<br />Filesystem 1K-blocks Used Available Use% Mounted on<br />/dev/vda2 15419956 2761756 11989780 19% /<br />GAMESS temporary binary files will be written to /tmp<br />GAMESS supplementary output files will be written to /tmp<br />Copying input file exam01.inp to your run's scratch directory...<br />cp exam01.inp /tmp/exam01.F05<br />unset echo<br />/usr/local/gamess/ddikick.x /usr/local/gamess/gamess.00.x exam01 -ddi 1 1 work -scr /tmp<br /><br /> Distributed Data Interface kickoff program.<br /> Initiating 1 compute processes on 1 nodes to run the following command:<br /> /usr/local/gamess/gamess.00.x exam01<br /><br /> ddikick.x: Timed out while waiting for DDI processes to check in.<br /> ddikick.x: Fatal error detected.<br /> The error is most likely to be in the application, so check for<br /> input errors, disk space, memory needs, application bugs, etc.<br /> ddikick.x will now clean up all processes, and exit...<br /> ddikick.x: Sending kill signal to DDI processes.<br /> ddikick.x: Execution terminated due to error(s).<br />unset echo<br />----- accounting info -----<br />Files used on the master node work were:<br />-rw-r--r-- 1 root root 1163 Sep 19 10:09 /tmp/exam01.F05<br />ls: No match.<br />ls: No match.<br />ls: No match.<br />Thu Sep 19 10:10:58 UTC 2019<br />0.0u 0.0s 1:01.11 0.0% 0+0k 0+8io 0pf+0w<br /><br /><br />Error - <br /> ddikick.x: Timed out while waiting for DDI processes to check in.<br /> ddikick.x: Fatal error detected.<br /> The error is most likely to be in the application, so check for<br /> input errors, disk space, memory needs, application bugs, etc.<br /> ddikick.x will now clean up all processes, and exit...<br /> ddikick.x: Sending kill signal to DDI processes.<br /> ddikick.x: Execution terminated due to error(s).<br />unset echo<br /><br />HOW CAN I FIX IT?Anonymoushttps://www.blogger.com/profile/11303770337597872931noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-3784245469108447152012-10-27T22:57:43.707+02:002012-10-27T22:57:43.707+02:00if you install GAMESS on personal computer. To avo...if you install GAMESS on personal computer. To avoid timeout error from DDI, a quick fix is to edit the line in the rungms file as<br /><br /> if ($NCPUS == 1) then<br /> set NNODES=1<br /> ## set HOSTLIST=(`hostname`)<br /> set HOSTLIST=127.0.0.1 ## 127.0.0.1 is just this PC<br /> endifAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-57028163151010400422012-10-09T12:26:26.418+02:002012-10-09T12:26:26.418+02:00how to do it?how to do it?rituparnahttps://www.blogger.com/profile/05296312451839035097noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-5420146297136597832012-10-09T12:25:05.905+02:002012-10-09T12:25:05.905+02:00I want to know is it possible to calculate only el...I want to know is it possible to calculate only electronic contribution to the electrostatic potential ( i.e., not the total ) on a particular atomic coordinate in GAMESS?rituparnahttps://www.blogger.com/profile/05296312451839035097noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-14016485556352926842012-06-07T14:52:20.531+02:002012-06-07T14:52:20.531+02:00Dear Jan please post how to compale (especially ed...Dear Jan please post how to compale (especially edit rungms) last US GAMESS 1 may 2012 on Linux. I tryed all but it stil dont work. Thank you before. I think many Gamess Users support me:)<br /><br />Best regardspropellanehttps://www.blogger.com/profile/00708576380803026822noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-13759314524216854682011-12-28T20:24:56.113+01:002011-12-28T20:24:56.113+01:00Dear Jan H. Jensen and Gamess Users,
I am trying ...Dear Jan H. Jensen and Gamess Users,<br /><br />I am trying to install Gamess on GPU in a computer with:<br /><br />S.O.: Linux - Ubuntu 11.04<br />Video Cards: 2 [GTX580 3GB/card]<br />Kernel version: 2.6.38-12 (x86_64)<br />Processor: i7 X 990 @ 3.47GHz<br />Intel Compilers Version: 12.0.5<br /><br />I am also installed :<br /><br />Cuda toolkit + SDK Version: 4.1 rc2 (release candidate)<br />Math Library: Atlas (from Ubuntu Repository)<br />Boost Version: 1.48.0<br />Cheetah Version: 2.4.4<br />HDF5 Version: 1.8.8<br />MPICH2 Version: 1.4.1p1<br /><br />PS: All the addons above were installed using intel compiler.<br /><br />The compilation procedure is running very well without any kind of<br />errors.<br /><br />But, the linking procedure is yielding the following error just in the<br />rhfuhf subroutine:<br /><br />=======================================<br />Choices for some optional plug-in codes are<br />Using qmmm.o, Tinker/SIMOMM code is not linked.<br />Using vbdum.o, neither VB program is linked.<br />Using neostb.o, Nuclear Electron Orbital code is not linked.<br /><br />message passing libraries are<br />../ddi/libddi.a -L/opt/mpich2_hydra/lib -lmpich -lmpl -lrt -lpthread<br /><br />other libraries to be searched are<br />-L/usr/lib64/atlas -lblas -latlas<br /><br />Linker messages (if any) follow...<br />rhfuhf.o: In function `rhfcl_':<br />rhfuhf.f:(.text+0x45ed): undefined reference to `molecule_new_gamess_'<br />rhfuhf.f:(.text+0x4604): undefined reference to `basis_new_gamess_'<br />rhfuhf.f:(.text+0x461b): undefined reference to `basis_sort_'<br />rhfuhf.f:(.text+0x4697): undefined reference to `hf_fock_'<br />rhfuhf.o: In function `cchem_hf_fock_':<br />rhfuhf.f:(.text+0x11c04): undefined reference to<br />`molecule_new_gamess_'<br />rhfuhf.f:(.text+0x11c2d): undefined reference to `basis_new_gamess_'<br />rhfuhf.f:(.text+0x11c56): undefined reference to `basis_sort_'<br />rhfuhf.f:(.text+0x11cab): undefined reference to `hf_fock_'<br /><br />Unfortunately, there was an error while linking GAMESS.<br />=======================================<br />Please take a look in my install.info file bellow:<br /><br />#!/bin/csh<br /># compilation configuration for GAMESS.GPU<br /># generated on langmuir<br /># generated at Sex Set 9 21:46:38 BRT 2011<br />setenv GMS_PATH /opt/gamess.gpu<br /># machine type<br />setenv GMS_TARGET linux64<br /># FORTRAN compiler setup<br />setenv GMS_FORTRAN ifort<br />setenv GMS_IFORT_VERNO 12<br /># mathematical library setup<br />setenv GMS_MATHLIB atlas<br />setenv GMS_MATHLIB_PATH /usr/lib64/atlas<br /># parallel message passing model setup<br />setenv GMS_DDI_COMM mpi<br />setenv GMS_MPI_PATH /opt/mpich2_hydra<br />setenv GMS_MPI_LIB mpich2<br /><br />=====================================<br /><br />Please could anyone help me ?<br /><br />Happy new year.<br /><br />Best regards,<br /><br />Sidney R. SantanaSidney Ramos Santanahttps://www.blogger.com/profile/01204822109692528461noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-36121238006372863992011-09-19T07:32:28.802+02:002011-09-19T07:32:28.802+02:00Heroy make sure all the "/mike" director...Heroy make sure all the "/mike" directories are changed to your home. <br /><br />also the /cu/mike <br /><br />jonAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-73534804454541849332011-08-05T12:36:22.001+02:002011-08-05T12:36:22.001+02:00A little tip:
On most linux PCs, you can make the...A little tip:<br /><br />On most linux PCs, you can make the "/sbin/sysctl -w kernel.shmmax=1610612736" command permanent, by adding the line <br /><br />"kernel.shmmax = 1610612736"<br /><br />to the file: /etc/sysctl.confAnonymoushttps://www.blogger.com/profile/18123073028209991396noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-81290957540593579582011-03-05T12:28:46.967+01:002011-03-05T12:28:46.967+01:00Thanks very much for your comment. I have updated...Thanks very much for your comment. I have updated the post accordingly.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-16183979007211462372011-03-04T14:27:34.144+01:002011-03-04T14:27:34.144+01:00Thanks for this compilation.
There is another nee...Thanks for this compilation.<br /><br />There is another needed step -- linked to propellane's problem above -- if your gamess installation does not reside in $HOME/gamess: the script checktst in tools/checktst must be edited to set GMSPATH to the correct path.<br /><br />Cheers,<br />MNMAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-20711702338914602192010-11-27T12:47:34.403+01:002010-11-27T12:47:34.403+01:00No idea what went wrong. I suggest posting to GAM...No idea what went wrong. I suggest posting to GAMESS mailing list with as many details about the installation, operating system, etc. as possible.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-56049944013955956392010-11-26T01:04:57.410+01:002010-11-26T01:04:57.410+01:00Dear Freinds
I just installed GAMESS and i got t...Dear Freinds <br /><br />I just installed GAMESS and i got the following errors <br /><br />exam27: sed: -e expression #1, char 3: invalid usage of line address 0<br />sed: -e expression #1, char 3: invalid usage of line address 0<br />Eerr=9.1e+00 Verr=2.9e-02. !!FAILED.<br />exam28: Eerr=9.0e+00. !!FAILED.<br />exam29: Eerr=2.3e+02. !!FAILED.<br />exam30: Eerr=1.7e+02 Gerr=8.2e-03. !!FAILED.<br />exam31: Eerr=1.2e+02 Gerr=3.3e-06 Ierr=7.9e-03. !!FAILED.<br />exam32: Eerr=1.3e+02 Terr=1.4e-02. !!FAILED.<br />exam33: Eerr=9.3e+01 Gerr=4.5e-02. !!FAILED.<br />exam34: Eerr=1.1e+02 Gerr=2.6e-02. !!FAILED.<br />exam35: Eerr=2.3e+03. !!FAILED.<br />exam36: Eerr=7.8e+01 Werr=3.2e+02 Ierr=1.1e+00. !!FAILED.<br />exam37: Eerr=2.2e+02 Gerr=2.7e-02. !!FAILED.<br />exam38: Eerr=1.2e+02 Gerr=1.0e-07. !!FAILED.<br />exam39: RIerr=1.2e+02 HRIerr=9.8e+02. !!FAILED.<br />exam40: E1err=3.9e+01 E2err=3.9e+01 RMSerr=4.0e-06 !!FAILED.<br />exam41: EXCerr=8.5e+00 eV, Gerr=1.1e-01, OSCerr=9.3e-02. !!FAILED.<br />exam42: Eerr=9.2e+01 Gerr=2.7e-02. !!FAILED.<br />exam43: HEATerr=1.8e+01 kcal/mol. !!FAILED.<br />exam44: SCFerr=6.0e+02 MP2err=6.0e+02. !!FAILED.<br />Only 0 out of 44 examples terminated normally.<br /><br /><br />thank You Hiruyhirhttps://www.blogger.com/profile/12022095139113902863noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-90289635955332137752010-11-01T09:41:06.927+01:002010-11-01T09:41:06.927+01:00Yes...
It’s Ok with 2 core… with "./rungms ex...Yes...<br />It’s Ok with 2 core… with "./rungms exam45.inp 00 2 >& exam45.log &" I got a normal termination.A.mayhttps://www.blogger.com/profile/10222439175602148977noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-85628460044316558492010-11-01T07:33:29.839+01:002010-11-01T07:33:29.839+01:00I am not sure what the problem is. I suggest post...I am not sure what the problem is. I suggest posting your question on the <a href="http://groups.google.com/group/gamess?hl=en" rel="nofollow">google GAMESS list</a>.<br /><br />When you post the question there, add more details, like whether exam45 is the only one you have problem with, and if it runs ok on 1 node, etc.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-40001242050874871802010-10-31T11:50:28.850+01:002010-10-31T11:50:28.850+01:00I type the following command to run exem45.inp on ...I type the following command to run exem45.inp on 4 core type(I have a quad core processor):<br />gamess@linux-84wt:~/gamess> ./rungms exam45 00 4 >& exam45.log &<br />I got <br />[2] 5335<br />[1] Done ./rungms exam45 00 2 >&exam45.log<br />The log files and like this:<br />unset echo<br />.//ddikick.x .//gamess.00.x exam45 -ddi 1 4 linux-84wt:cpus=4 -scr ./<br /><br /> Distributed Data Interface kickoff program.<br /> Initiating 4 compute processes on 1 nodes to run the following command:<br /> .//gamess.00.x exam45 <br /><br /> TCP connect error: ENETUNREACH.<br /> DDI Process 1: error code 911<br /> TCP: Connect failed. linux-84wt -> localhost:36474.<br /> ddikick.x: application process 1 quit unexpectedly.<br /> ddikick.x: Fatal error detected.<br /> The error is most likely to be in the application, so check for<br /> DDI Process 0: error code 911<br /> DDI Process 0: TCP Error in Recv.<br /> TCP recv error: Unknown.<br /> TCP recv error: return value errno=-97851104<br /> DDI Process 2: terminated upon request.<br /> DDI Process 3: terminated upon request.<br /> ddikick.x: Sending kill signal to DDI processes.<br /> ddikick.x: Execution terminated due to error(s).<br />unset echo<br />----- accounting info -----<br />Files used on the master node linux-84wt were:<br />-rw-r--r-- 1 gamess users 2197 oct 30 22:41 .//exam45.F05<br />-rw-r--r-- 1 gamess users 2197 oct 30 22:36 .//exam45.inp<br />-rw-r--r-- 1 gamess users 4509 oct 30 22:41 .//exam45.log<br />sam oct 30 22:41:46 CET 2010<br />0.132u 0.048s 0:01.22 13.9% 0+0k 0+0io 0pf+0w<br />I think that isn’t work properly, sir any help is appreciate<br /><br />May abdelghaniA.mayhttps://www.blogger.com/profile/10222439175602148977noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-40878183906166606092010-10-20T09:20:13.241+02:002010-10-20T09:20:13.241+02:00Thank you very much for this info. I have added a...Thank you very much for this info. I have added a link to your comment on the post.<br /><br />I am happy to hear you like the blog.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-48664950419462763642010-10-19T23:43:35.467+02:002010-10-19T23:43:35.467+02:00Great post, and superb blog to start fiddling with...Great post, and superb blog to start fiddling with GAMESS. Just note that linux kernels above 2.6.28 to 2.6.32 will give an error in exam32, as pointed out here: http://www.chemsoft.ch/qc/ubuntumake.htm<br /><br />I think it is worth to make a short mention of this in the text, since many popular distributions (Ubuntu 9.10 and 10.04, Linux Mint 8 and 9, Knoppix 6.2.1 or Suse 11.2) have included this faulty kernels until recently and probably there are still users running them. They should be aware of this problem (to avoid them scratching their heads for hours wondering what went wrong)and should be encouraged to upgrade their distribution to the latest version -or at least upgrade the kernel to a higher version (>=2.6.33).<br /><br />Well, thanks for your work!Unknownhttps://www.blogger.com/profile/06869838275928552806noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-53420525796282620812010-10-13T19:27:19.019+02:002010-10-13T19:27:19.019+02:00Jan you are Genius thank you very much)) i did so ...Jan you are Genius thank you very much)) i did so i writed '/home/propellane/games' in GMSPATH in checktsts file then run chektsts and it work all passed)). Thank you for quick reply! Early i used PC gamess (firefly) in Windows, but now have some problems on my OpenSuSe 11.3 (problems i suppose in kernel). <br />About Priroda this DFT free programm maybe its not strong ab initio programm, but it gives great results with organic compounds especially carbocation also it give correct nmr shift. I used it as black box, count some parent ethalon structures and then my structures. i can give some info maybe youllbe interested http://www.qchem.ru/f/kvantovo-khimicheskie-programmy/kvantovo-khimicheskaya-programma-priroda/ -There are some english publications<br /><br />P.S. Waiting your new greate postspropellanehttps://www.blogger.com/profile/00708576380803026822noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-64066034406332580452010-10-13T16:58:55.776+02:002010-10-13T16:58:55.776+02:00The script is looking for the log files in /root/g...The script is looking for the log files in /root/gamess/tools/checktst/.<br /><br />If you are logged in as root, try loggin in as propellane instead.<br /><br />I assume you have verified that your files actually are in /home/propellane/gamess/Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-62775972766421862842010-10-13T16:02:00.803+02:002010-10-13T16:02:00.803+02:00Thank you, Jan for good job! it's really usefu...Thank you, Jan for good job! it's really useful for such noob as me, but when i tried to run checktst i've got the next notice:<br /> <br />Checking the results of your sample GAMESS calculations,<br />the output files (exam??.log) will be taken from /home/propellane/gamess/<br />All jobs terminated normally, now checking detailed numerical results<br />exam01: /root/gamess/tools/checktst/exam01: Команда не найдена.<br />!!FAILED.<br />exam02: /root/gamess/tools/checktst/exam02: Команда не найдена.<br />!!FAILED.<br />exam03: /root/gamess/tools/checktst/exam03: Команда не найдена.<br />..............................................................<br />44 job(s) got incorrect numerical results. Please examine why<br /><br />Then i changed path in checktst (default GSMPATH=~/gamess) i tried ./ and . Even i took exact directory /home/propellane/gamess/tools/checktst/tools/checktst/ but i've get an get same result<br /><br />!!FAILED.<br />exam03: /home/propellane/gamess/tools/checktst/tools/checktst/exam03: Команда не найдена.<br />!!FAILED<br /><br />So where is wrong? Thank you very much before for replying<br /><br />P.S. Команда не найдена - Command is no found (in translation in russian)propellanehttps://www.blogger.com/profile/00708576380803026822noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-49714185489660154832010-08-31T07:29:13.635+02:002010-08-31T07:29:13.635+02:00I had not seen this site before. Thanks very much...I had not seen this site before. Thanks very much for pointing it out to me. <br /><br />Glad to hear you like the blog.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-85660617027094418472010-08-31T06:36:26.348+02:002010-08-31T06:36:26.348+02:00Hello.
In this website there are some script...Hello.<br /> In this website there are some scripth to install GAMESS on linux distro by only running them http://www.chemsoft.ch/qc/gamkpx.htm, I installed GAMESS in ubuntu, fedora and Centos without a problem. Thank you for this website Dr Jensen.<br /><br />yours<br />Rubén Fritz.The_Shuishttps://www.blogger.com/profile/15614015867896367335noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-39012034054728065872010-08-30T16:44:00.163+02:002010-08-30T16:44:00.163+02:00You're welcome. Thanks for the link, which is...You're welcome. Thanks for the link, which is now included on the post.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-1345961324987514302010-08-30T13:27:28.658+02:002010-08-30T13:27:28.658+02:00Hi
Thanks for your attention to my request.
Please...Hi<br />Thanks for your attention to my request.<br />Please see this page: <br />http://gamess-linux.blogspot.com/<br />If you think it is useful, please put a link for this page too.<br />Best regards<br />AlchemistAnonymousnoreply@blogger.com