[Dock-fans] Dock-fans Digest, Vol 57, Issue 1
thaniks
kthanikasalam at gmail.com
Thu Feb 5 02:22:36 PST 2009
Dear dock friends,
I am new to dock 6.0. I am using windows vista and cygwin
in HP system. While i am trying to install dock 6.0. i got the following
error and also please let me know what gnu i have to configure for my
computer.
* Error *(I copied it from cygwin window and pasted here)
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
$ make all
Starting installation of
DOCK v6.2
at Thu Feb 5 15:41:17 IST 2009.
cd ../src && make install
make[1]: Entering directory `/dock6/src'
cd dock && make install
make[2]: Entering directory `/dock6/src/dock'
g++ -c -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -I/include
-DBUILD_DOCK_WI
TH_ZAP -I -O2 -o amber_typer.o amber_typer.cpp
make[2]: g++: Command not found
make[2]: *** [amber_typer.o] Error 127
make[2]: Leaving directory `/dock6/src/dock'
make[1]: *** [dock6] Error 2
make[1]: Leaving directory `/dock6/src'
make: *** [install] Error 2
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Please Help me to solve this problem
K. Thanikasalam
On Thu, Feb 5, 2009 at 1:30 AM, <dock-fans-request at docking.org> wrote:
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> Today's Topics:
>
> 1. dock6 jobs using 7 cpu mins, but run for 15 hours.
> (Mary Ellen Fitzpatrick)
> 2. hi (thaniks)
> 3. Re: hi (John J. Irwin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 04 Feb 2009 11:17:33 -0500
> From: Mary Ellen Fitzpatrick <mfitzpat at bu.edu>
> Subject: [Dock-fans] dock6 jobs using 7 cpu mins, but run for 15
> hours.
> To: dock-fans at docking.org, Mary Ellen Fitzpatrick <mfitzpat at bu.edu>
> Message-ID: <4989BF9D.7070603 at bu.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> I have a dual-dual core Opteron cluster running Cento5, torque-2.3.6,
> maui-3.2.6p21, mpich2-1.0.8(64bit) and parallel dock6.
> I installed dock6 serial as 32-bit, then installed dock6 parallel as
> 32-bit.
>
> I have configured my queues and scripts to run the dock mpi jobs and
> they do run to completion without errors.
>
> The problem I am seeing is that my mpi job is running for a total of
> 15hours, but is using only ~ 7minutes of cputime.
> outfile
> Limits: ncpus=4,neednodes=1,nodes=1,walltime=48:00:00
> Resources: cput=00:06:55,mem=9964kb,vmem=279836kb,walltime=15:12:46
>
> When the job is running, I log into the node, and can see the cpu's at
> 100%, so it is not sitting idle and there is not an nfs traffic to speak
> of.
>
> Anyone run into this issue before? Is this an mpi issue?
>
> --
> Thanks
> Mary Ellen
>
> --
> Thanks
> Mary Ellen
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 4 Feb 2009 22:47:35 +0530
> From: thaniks <kthanikasalam at gmail.com>
> Subject: [Dock-fans] hi
> To: dock-fans at docking.org
> Message-ID:
> <a2e182280902040917k30a4eb69nbc40de371f6f745d at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> I am K. Thanikasalam. I am new to DOCK6.0. I want to install Dock 6.0 in
> windows vista (HP) laptop. Please let me know the installation commands or
> procedures or any tutorial for this installation. I already have cygwin in
> my system. any help in this greatly acknowledged.
>
> ---
> with thanks and love
>
> K. Thanikasalam
> Research Associate
> Department of Chemistry
> Indian Institute of Technology - Madras
> Chennai
>
>
> Ph. No. 09994559987 (mob)
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> ------------------------------
>
> Message: 3
> Date: Wed, 04 Feb 2009 09:27:24 -0800
> From: "John J. Irwin" <jji at cgl.ucsf.edu>
> Subject: Re: [Dock-fans] hi
> To: thaniks <kthanikasalam at gmail.com>
> Cc: dock-fans at docking.org
> Message-ID: <4989CFFC.5030208 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi -
>
> Please look here for DOCK on Windows under cygwin:
> http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_on_cygwin
>
> Good docking!
>
> John
>
>
> thaniks wrote:
> > Hi,
> > I am K. Thanikasalam. I am new to DOCK6.0. I want to install Dock 6.0
> > in windows vista (HP) laptop. Please let me know the installation
> > commands or procedures or any tutorial for this installation. I
> > already have cygwin in my system. any help in this greatly acknowledged.
> >
> > ---
> > with thanks and love
> >
> > K. Thanikasalam
> > Research Associate
> > Department of Chemistry
> > Indian Institute of Technology - Madras
> > Chennai
> >
> >
> > Ph. No. 09994559987 (mob)
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
>
>
> ------------------------------
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
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>
>
> End of Dock-fans Digest, Vol 57, Issue 1
> ****************************************
>
--
with thanks and love
K. Thanikasalam
Research Associate
Department of Chemistry
Indian Institute of Technology - Madras
Chennai
Ph. No. 09994559987 (mob)
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