[Dock-fans] Dock-fans Digest, Vol 57, Issue 1
John J. Irwin
jji at cgl.ucsf.edu
Fri Feb 6 16:41:25 PST 2009
you need to install the "devel" tools as per
http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_on_cygwin
which includes gcc and g++.
Good docking
John
thaniks wrote:
> 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
> <mailto: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
> <mailto:mfitzpat at bu.edu>>
> Subject: [Dock-fans] dock6 jobs using 7 cpu mins, but run for 15
> hours.
> To: dock-fans at docking.org <mailto:dock-fans at docking.org>, Mary
> Ellen Fitzpatrick <mfitzpat at bu.edu <mailto:mfitzpat at bu.edu>>
> Message-ID: <4989BF9D.7070603 at bu.edu <mailto: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
> <mailto:kthanikasalam at gmail.com>>
> Subject: [Dock-fans] hi
> To: dock-fans at docking.org <mailto:dock-fans at docking.org>
> Message-ID:
>
> <a2e182280902040917k30a4eb69nbc40de371f6f745d at mail.gmail.com
> <mailto: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)
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 04 Feb 2009 09:27:24 -0800
> From: "John J. Irwin" <jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>>
> Subject: Re: [Dock-fans] hi
> To: thaniks <kthanikasalam at gmail.com <mailto:kthanikasalam at gmail.com>>
> Cc: dock-fans at docking.org <mailto:dock-fans at docking.org>
> Message-ID: <4989CFFC.5030208 at cgl.ucsf.edu
> <mailto: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 <mailto:Dock-fans at docking.org>
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
>
>
> ------------------------------
>
> _______________________________________________
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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)
> ------------------------------------------------------------------------
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
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