Re: [Apbs-users] problem with installing apbs with maloc
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Re: [Apbs-users] problem with installing apbs with maloc
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From: LIANG MA <lm...@wi...> - 2007-06-01 16:17:10
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Dear Michael, Sure, Thanks. ----- Original Message ----- From: Michael Holst <mh...@ma...> Date: Friday, June 1, 2007 12:18 am Subject: Re: [Apbs-users] problem with installing apbs with maloc To: Nathan Baker <sob...@gm...> Cc: LIANG MA <lm...@wi...>, David Gohara <sd...@gm...>, apb...@li..., Mike Holst <mh...@ma...> > Dear Liang (and I guess the entire apbs-users email list), > > We are very close to putting the first public release of FETK out. > Can you check back again in about three weeks? > > best regards, -mike > > Nathan Baker <sob...@gm...> (05-29-2007 13:38:12-0500): > >Hi Liang -- > > > >Mike Holst can provide more information about availability; I'll Cc him. > > > >Thanks, > > > >Nathan > > > >On May 29, 2007, at 1:30 PM, LIANG MA wrote: > > > >>Hi Nathan and Dave, > >> There is still a problem. I couldn't find any link to MC > >>source code on the fetk.org. It just says "The MC source code will > > >>be available in Fall 2006" under obtaining MC section. Do you know > > >>where I can get it. > >> Thanks! > >>Liang > >>----- Original Message ----- > >>From: Nathan Baker <sob...@gm...> > >>Date: Tuesday, May 29, 2007 6:55 am > >>Subject: Re: [Apbs-users] problem with installing apbs with maloc > >>To: LIANG MA <lm...@wi...> > >>Cc: David Gohara <sd...@gm...>, apb...@li... > >> > >> > >>>Hi Liang -- > >>> > >>>> Thanks a lot. Yes, the installation without --with-fetk-library > >>> > >>>>does work. > >>> > >>>That's good! > >>> > >>>>But I want to use fe-manual (the finite element method) to solve > >>>>PB. For this purpose, do I need MALOC only or the full FETK package? > >>> > >>>You need the full FEtk package. > >>> > >>>>If the latter is ture, could you please suggest the packages of > >>>>FETK to install and installing procedure for APBS? > >>> > >>>APBS requires the FEtk MC (http://www.fetk.org/codes/mc/index.html) > >>>and PUNC (http://www.fetk.org/codes/punc/index.html). > >>> > >>>Thanks, > >>> > >>>Nathan > >>> > >>>> Thanks, > >>>>Liang > >>>> > >>>>----- Original Message ----- > >>>>From: David Gohara <sd...@gm...> > >>>>Date: Monday, May 28, 2007 7:17 pm > >>>>Subject: Re: [Apbs-users] problem with installing apbs with maloc > >>>>To: LIANG MA <lm...@wi...> > >>>>Cc: apb...@li... > >>>> > >>>> > >>>>>Hi Liang, > >>>>> > >>>>> Are you trying to build against MALOC only or the full FETK. If > >>> > >>>>>you > >>>>> are only in need of MALOC, then you do not (and should not) > >>>>>specify > >>>>> --with-fetk-library. We now include a distribution of MALOC > >>>>>with the > >>>>> APBS source code. So your procedure should be something like this: > >>>>> > >>>>> ./configure --prefix=/path/to/install > >>>>> make > >>>>> make install > >>>>> > >>>>> Hope that helps, > >>>>> > >>>>> Dave > >>>>> > >>>>> On 5/28/07, LIANG MA <lm...@wi...> wrote: > >>>>>>Hi Nathan and all, > >>>>>> I was trying to install apbs with maloc on a linux machine. > >>>>>Maloc was installed successfully. I configured apbs with linking > to > >>>>>the maloc library and include files as follows: > >>>>>>./configure --with-fetk-include=${FETK_PREFIX}/include > >>>>>--with-fetk-library=${FETK_PREFIX}/lib/i686-pc-linux-gnu/ > >>>>>--prefix=/home/ma/program/apbs_install | & tee conf.log, where > >>>>>FETK_PREFIX is the directory under which I installed maloc. > >>>>>> However, there is a problem when I tried to run make; it > > >>>>>>says > >>>>>"ld: cannot find -lapbsblas", which seems that this option for > >>>>>linking > >>>>>is not recognized. Here I need some help. > >>>>>> I also attached the conf.log and make.log file. > >>>>>> Thanks in advance! > >>>>>> > >>>>>>Liang > >>>>>> > >>>>>> > >>>-------------------------------------------------------------------- > >>>>>>----- > >>>>>>This SF.net email is sponsored by DB2 Express > >>>>>>Download DB2 Express C - the FREE version of DB2 express and take > >>>>>>control of your XML. No limits. Just data. Click to get it now. > >>>>>>http://sourceforge.net/powerbar/db2/ > >>>>>>_______________________________________________ > >>>>>>apbs-users mailing list > >>>>>>apb...@li... > >>>>>>https://lists.sourceforge.net/lists/listinfo/apbs-users > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> David W. Gohara, Ph.D. > >>>>> Center for Computational Biology > >>>>> Washington University School of Medicine > >>>>> http://gohara.wustl.edu > >>>>> http://www.macresearch.org > >>>>> 314-362-1583 (phone) <=== NEW New Number > >>>>> 617-216-8616 (cell) > >>>>> > >>>> > >>>> > >>>--------------------------------------------------------------------- > > >>>- > >>> > >>>>--- > >>>>This SF.net email is sponsored by DB2 Express > >>>>Download DB2 Express C - the FREE version of DB2 express and take > >>>>control of your XML. No limits. Just data. Click to get it now. > >>>>http://sourceforge.net/powerbar/db2/ > >>>>_______________________________________________ > >>>>apbs-users mailing list > >>>>apb...@li... > >>>>https://lists.sourceforge.net/lists/listinfo/apbs-users > >>> > >>>-- > >>>Associate Professor, Dept. of Biochemistry and Molecular Biophysics > >>>Center for Computational Biology, Washington University in St. Louis > >>>Web: http://cholla.wustl.edu/ > >>> > >>> > > > >-- > >Associate Professor, Dept. of Biochemistry and Molecular Biophysics > >Center for Computational Biology, Washington University in St. Louis > >Web: http://cholla.wustl.edu/ > > > End of message from Nathan Baker. > > -- > Michael Holst, Ph.D. > Professor of Mathematics Phone: (858) 534-4899 > UNIVERSITY OF CALIFORNIA, SAN DIEGO Fax: (858) 534-5273 > Department of Mathematics, 5739 AP&M Email: mh...@ma... > 9500 Gilman Drive, Dept. 0112 Net: http://cam.ucsd.edu/~mholst > La Jolla, CA 92093-0112 USA > > Senior Scientist, NSF CTBP Center < > Core Investigator, NIH NBCR Resource < > Co-Director, CSME Graduate Program < > -- |