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-- B. Lachele Foley, PhD '92,'02 Assistant Research Scientist Complex Carbohydrate Research Center, UGA 706-542-0263 lfoley.ccrc.uga.edu ----- Original Message ----- From: Lachele Foley [mailto:lfoley.ccrc.uga.edu] To: AMBER Developers Mailing List [mailto:amber-developers.ambermd.org] Sent: Wed, 12 May 2010 14:05:42 -0400 Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in Ubuntu 9.10 > And, uhm... recompiling. Results tomorrow, maybe. > > > :-) Lachele > -- > B. Lachele Foley, PhD '92,'02 > Assistant Research Scientist > Complex Carbohydrate Research Center, UGA > 706-542-0263 > lfoley.ccrc.uga.edu > > > ----- Original Message ----- > From: Lachele Foley > [mailto:lfoley.ccrc.uga.edu] > To: AMBER Developers Mailing List > [mailto:amber-developers.ambermd.org] > Sent: Wed, 12 May 2010 14:03:40 > -0400 > Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in > Ubuntu 9.10 > > > > Actually... it's the other compiler. But, not for lack of trying. > > > > I totally did not expect this... > > > > Here, the user has gcc aliased at login: > > > > [installer.aarya src]$ which gcc > > gcc: aliased to /usr/bin/gcc44 > > [installer.aarya src]$ gcc --version > > gcc44 (GCC) 4.4.0 20090514 (Red Hat 4.4.0-6) > > > > ...but the config is finding something different... > > > > ======================================================== > > [installer.aarya src]$ ./configure gnu > > Your AMBERHOME environment variable should be set to > > /usr/local/programs64/amber11 > > > > > > Obtaining the gnu suite version: > > gcc -v > > The version is 4.1.2 > > ======================================================== > > > > GAAAAUUUGHHHHH!!!! > > Is it because the script is in sh? > > > > > > It obviously pays attention to the .cshrc file, because when I made a > > directory $HOME/bin, set that first in the path, with sym links inside to > > the various places, it found the right compilers. > > > > sh doesn't recognize the term "alias"... > > > > :-) Lachele > > -- > > B. Lachele Foley, PhD '92,'02 > > Assistant Research Scientist > > Complex Carbohydrate Research Center, UGA > > 706-542-0263 > > lfoley.ccrc.uga.edu > > > > > > ----- Original Message ----- > > From: Volodymyr Babin > > [mailto:vbabin.ncsu.edu] > > To: AMBER Developers Mailing List > > [mailto:amber-developers.ambermd.org] > > Sent: Wed, 12 May 2010 13:15:12 > > -0400 > > Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in > > Ubuntu 9.10 > > > > > > > Hi Lachele, > > > > > > thank you. It might be indeed something else. If it fails again with > > > 4.4.0, please give me the outputs [or .diff(s)] to look at. I am not > > > sure to what extent this can be relevant, but 'man alias' says > > > > > > ... > > > the alias definition shall not affect the parent process of the current > > > shell nor any utility environment invoked by the shell; see Shell > > Exe‐ > > > cution Environment > > > ... > > > > > > and it thus may be worthwhile to try making 'gcc->gcc44' symlinks > > > somewhere and then add this somewhere to the front of the PATH. > > > > > > Thank you & best regards, > > > > > > Volodymyr > > > > > > On Wed, May 12, 2010 12:03, Lachele Foley wrote: > > > > 4.4.0 > > > > > > > > I'll have her re-do from a clean un-tar (even if she did this time), > > just > > > > to be sure. I checked her paths. She has gcc aliased to > /usr/bin/gcc44 > > > > and so forth, and gcc --version yields 4.4.0, etc. The MPI execs all > > just > > > > point to "gcc", so they should go wherever her gcc points. > > > > > > > > It might not be RHEL. Could be the machine. Has an AMD processor... > > any > > > > chance that matters? > > > > > > > > :-) Lachele > > > > -- > > > > B. Lachele Foley, PhD '92,'02 > > > > Assistant Research Scientist > > > > Complex Carbohydrate Research Center, UGA > > > > 706-542-0263 > > > > lfoley.ccrc.uga.edu > > > > > > > > > > > > ----- Original Message ----- > > > > From: case > > > > [mailto:case.biomaps.rutgers.edu] > > > > To: AMBER Developers Mailing List > > > > [mailto:amber-developers.ambermd.org] > > > > Sent: Wed, 12 May 2010 11:49:33 > > > > -0400 > > > > Subject: Re: [AMBER-Developers] sander.MPI tests randomly stall in > > > > Ubuntu 9.10 > > > > > > > > > > > >> On Wed, May 12, 2010, Lachele Foley wrote: > > > >> > > > >> > > > > >> > The failures are all from the ncsu set: > > > >> > > > >> Is this with gcc 4.1.2 or gcc 4.4.0? The ncsu errors with 4.1.2 are > > > >> well > > > >> known (and will probably never be fixed); if you had errors with > 4.4.0, > > > >> it would be of interest to know what they are. I've used gcc44 on > > > >> Ubuntu > > > >> and on CentOS with no such failures, fwiw. > > > >> > > > >> ....thx...dave > > > >> > > > >> > > > >> _______________________________________________ > > > >> AMBER-Developers mailing list > > > >> AMBER-Developers.ambermd.org > > > >> http://lists.ambermd.org/mailman/listinfo/amber-developers > > > >> > > > > > > > > _______________________________________________ > > > > AMBER-Developers mailing list > > > > AMBER-Developers.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber-developers > > > > > > > > > > > > > _______________________________________________ > > > AMBER-Developers mailing list > > > AMBER-Developers.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber-developers > > > > > > > _______________________________________________ > > AMBER-Developers mailing list > > AMBER-Developers.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber-developers > > > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers > _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Fri May 14 2010 - 19:00:03 PDT