fatal error chdir failed namd Huntington Park California

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fatal error chdir failed namd Huntington Park, California

Locating benchmarks...found 31 benchmarks in 3 benchsets. How do you do that on a cluster running clustermatic? What does it mean? (On a side note, I have found that it is possible to bypass this issue through cd $(pwd).) linux unix share|improve this question asked Nov 20 '13 [email protected]:~$ sudo apt-get install gfortran libblas-dev libatlas-base-dev Note: your atlas libraries will be installed in /usr/lib64/atlas/ - this will matter when you run config.

The rawformat utility is also automatically invoked by runspec at the end of a run, to generate the reports from your run. This, for instance, would make rungms modification much easier. Please type ‘gfortran -dumpversion' or else ‘gfortran -v' to detect the version number of your gfortran. CRYST1 1.000 1..000 1.000 90.00 90.00 90.00 P 1 1 ATOM 1 O5' C A X 1 1.477 -17.625 15.716 1.00 0.69 O ATOM 2 C5' C A X 1 2.783

Allis, PhD 2 weeks ago “Upstate NY Stargazing In October” is up at @syracusedotcom (syracuse.com/outdoors/index…) & @newyorkupstate (newyorkupstate.com/outdoors/2016/…) [email protected] Damian G. Furthermore, we must change GMSPATH from how the ever-helpful Mike Schmidt (he got me through some early issues when I started my GAMESS-US adventure 15ish years ago. The slave nodes have only a very basic operating system which is booted from a CD. Note: 'go' does not know about your settings for output_root or expid, and will not be able to take you to your run, exe, or result directories if you use those

For CPU2006 V1.0 and V1.1, you needed to remove previous outputs by hand before your run in order to avoid confusion from output files (e.g. .mis) that were hanging around from Allis, PhD 1 week ago Someday, Ubuntu Desktop will truly be ready for primetime. If you are doing both development work and reportable runs, install the suite twice in two different directory trees (for example, on different disks). Benchmark 464.h264ref has a code "r?" for the Reference workload with the base tuning, indicating a run-time failure.

Allis, PhD [email protected] Damian G. You could examine "speccmds.out", but that file is not easy to interpret: $ runspec --config=try_utilities --size=test --iterations=1 \ --tuning=base --output_format=ps 400 $ go work 400 $ cd run_base_test_try_utilities.0000/ $ $ cat There are also commercial compilers, namely Intel's ‘ifort', Portland Group's ‘pgfortran', and Pathscale's ‘pathf90'. Downloading GAMESS-US, Placing Into /opt, And Changing Permissions First, obviously, get the GAMESS source (click on the red text).

Thanks a lot, Gianluca ----------------------------------------------------- Dr. For example, depending on your operating system and your shell, you might be able to enter a command such as: export http_proxy=http://www-prox Skip to content welcome to somewhereville.com population 1; For example: $ pwd /rahul/benchspec/CPU2006/401.bzip2/run/build_base_a3.0000 $ go exe /rahul/benchspec/CPU2006/401.bzip2/exe $ go also understands -h and --help, and will output a short usage message in response to either of those arguments. Post navigation Previous Previous post: CudaMiner Installation In Ubuntu 12.04 LTS Using CUDA Toolkit 5.5 And "Additional NVIDIA Drivers"Next Next post: Play Softly And Carry A Thin Pair Of Sticks, Or

If you try to apply the output of dumpsrcalt yourself, take care to notice how paths are handled by your patch program, especially if the src.alt is for a benchmark that You must also put a file named "README" in that subdirectory. If this was my biggest concern I'd be a happy quantum chemist. You can send the output to a file, which can then be easily edited.

Locating benchmarks...found 31 benchmarks in 2 benchsets. drwxr-xr-x 14 1300 5044096 2014-04-04 21:43 gamess -rw-r-r- 1 rootroot198481920 2014-04-04 21:42 gamess-current.tar Which you remedy before running into this error by changing the permissions: [email protected]:/opt$ sudo chown -R username gamess MOLECULE MISSING! However, the master node is always included per default and to avoid that I'm trying to use the flag "++skipmaster".

[email protected] Damian G. If you attempt to use the flag_dump utility to format any of the suite-provided flag files such as flags_mandatory.xml or the benchmark flag files that reside in $SPEC/benchspec/CPU2006/*/Spec/ directory, the utility Meantime, default value is fine. [enter] 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 FATAL ERROR: chdir() failed!

Sadly, today is not that day. #nodisrespect #dontencrypttheweholedriveandupdate [email protected] Damian G. or(Mon Dec 08 2008 - 03:36:50 CST) Re: namd2 erratic performance over 104 procs(Sat Dec 06 2008 - 03:18:29 CST) Re: regarding writemol2(Fri Dec 05 2008 - 03:13:48 CST) Re: mpirun Molec. Each node has a harddrive but it is not used.

Would you still get a stale file handle? Te, Tr, and Ref indicate the Test, Train, and Ref workloads. Worked my way through the following from the notes/readmes: [quote] npack NAMD and matching Charm++ source code and enter directory: tar xzf NAMD_2.7b2_Source.tar.gz cd NAMD_2.7b2_Source tar xf charm-6.1.3.tar cd charm-6.1.3 Build A train station is where a train stops.

Can anyone help please?? The dumpsrcalt tool allows you to find out what's in a src.alt without necessarily having to apply it. Unfortunately, this gives me the error "FATAL ERROR: chdir() failed!". CHARMM.

Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html Unlimited freedom, unlimited storage. Cafe Scientifique: “What Do Rockets And Steamboats Have In Common? You can quit at any time by pressing control-C, and then . Note: It's not necessary to export the "GO" variable.

The log for this run is in /cpu2006/dr_evil/result/CPU2006.009.log runspec finished at Thu May 25 10:01:54 2006; 8 total seconds elapsed $ Sure enough, it failed. Break a non-dominant leg! Old build directories should be deleted (perhaps after backing them up if you wish to save them for reference). Let's find the appropriate run directory where our silly build was attempted: $ go leslie3d run /cpu2006/dr_evil/benchspec/CPU2006/437.leslie3d/run $ ls build_base_silly.0000 list $ cd build_base_silly.0000 And ask specmake just exactly what it

relocate (Unix only) If you rearrange mount points or rename your SPEC root directory, you will probably find confusing problems like the one in the example that follows. If you'd like for the filename of the extracted flags file to match the rawfile, use the --nofilename option. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. In addition, you will get the formats that you mention on the command line, or, if none are mentioned there, then you will get the defaults documented under output_format. (History: the

You can check this yourself by running top in another window. Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work Once you have your flags file passing specrxp validation, you should do a flag_dump, and validate that the dump is valid HTML.