[gmx-users] Installation on IBM A.I.X.5.2.0.0
Li Zhenhai
shibalagu.thu at gmail.com
Fri Nov 30 05:21:19 CET 2007
Dear GMX users:
I met a trouble when I installed Gromacs on IBM A.I.X 5.2.0.0, and I still failed to install it after I checked the mailing list and found ways to fix my problem. So I want to list my problem here beging for your helps.
I installed the fftw. And the installation finished successfully. The order I used is showed below.
export CC=xlc;
export MPICC=mpcc;
export F77=xlf;
export CXX=xlC;
export CFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -w"
export FFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qansialias -qstrict -w"
./configure --enable-type-prefix --prefix=.../fftw312
make
make install
./configure --enable-type-prefix --prefix=.../fftw312 --enable-float
make
make install
Then, with environment parameters above unchanged, and adding these parameters, I startet to install a serial Gromacs.
export CPPFLAGS=-I .../fftw312/include
export LDFLAGS=-L .../fftw312/lib
The step below can finish successfully
./configure --prefix=.../gmx33 --exec-prefix=.../gmx33 --enable-float --disable-fortran --disable-largefile --without-x --disable-vectorized-sqrt
But when I typed the order "make", It would stop with saying:
"gmx_fft_fftw3.c", line 186.8: 1506-068 (S) Operation between types "void*" and "int" is not allowed.
"gmx_fft_fftw3.c", line 190.8: 1506-068 (S) Operation between types "void*" and "int" is not allowed.
And if I install a parallel Gromacs. It cannot finish the "configure" step with saying:
"cannot calculate the size of 'int'"
And I checked the config.log. And found that there was some problem on "conftest.c" like this:
configure:2954: xlc_r -c -I/u/lixy/bin/fftw/include conftest.c >&5
"conftest.c", line 22.14: 1506-275 (S) Unexpected text me encountered.
"conftest.c", line 22.8: 1506-045 (S) Undeclared identifier choke.
configure:2960: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "GROMACS"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "3.3.1"
| #define PACKAGE_STRING "GROMACS 3.3.1"
| #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "3.3.1"
| #define GMX_FORTRAN
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Thu Mar 29 03:28:25 GMT 2007"
| #define BUILD_USER "lixy at d35n01"
| #define BUILD_MACHINE "AIX 2 0025EECD4C00"
| /* end confdefs.h. */
|
| int
| main ()
| {
| #ifndef __GNUC__
| choke me
| #endif
|
| ;
| return 0;
| }
configure:2986: result: no
And I also change the environment as below, but I met the same error.
export CC=xlc;
export MPICC=mpcc;
export F77=xlf;
export CXX=xlC;
export CFLAGS="-O2 -qarch=pwr2 -qtune=pwr2"
export FFLAGS="-O2 -qarch=pwr2 -qtune=pwr2"
Could anybody here help me. Any more ideas would be very much appreciated.
Li Zhenhai
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
China
Tel: 86-10-62773779
E-mail: shibalagu.thu at gmail.com
2007-11-30
======= 2007-11-30 05:36:22 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======
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>Today's Topics:
>
> 1. Re: osmotic pressure in Gromacs (David van der Spoel)
> 2. Re: gmxtest seems to have missing files (David van der Spoel)
> 3. osmotic pressure in Gromacs (chris.neale at utoronto.ca)
> 4. Re: Double precision test failure (David van der Spoel)
> 5. Re: rtp file (özge kül)
> 6. Re: rtp file (Justin A. Lemkul)
> 7. Re: Double precision test failure (Chris Snook)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 29 Nov 2007 19:02:57 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] osmotic pressure in Gromacs
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <474EFED1.4020501 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=GB2312
>
>º¼¾ü ½ wrote:
>> Hi,
>>
>> */ We want to simulate water transport through channel by osmotic
>> pressurce using Gromacs software. The force on the water molecules is
>> usually applied only in a buffer zone, not on all water molecules. How
>> to set up my system. In my opion, we can only define a simple group by
>> index. Water molecules are moving, so the water molecules in a buffer
>> zone change frequently. How to define the group of water molecules in a
>> buffer zone. Gromacs can do it?/*
>> */ thanks!/*
>
>Of course. How do you model the channel?
>If you put two membranes like this:
>
>Water
>
>=== membrane ====
>
>Water with salt
>
>=== membrane ====
>
>Water (periodic)
>
>the membrane will probably break sponteously. Look for papers by Ilpo
>Vattulainen on this topic.
>
>
>>
>> ÑÅ»¢ÓÊÏ䣬ÖÕÉú»ï°é£¡
>> <https://member.cn.yahoo.com/cnreg/reginfo.html?id=89034>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>--
>David van der Spoel, Ph.D.
>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
>------------------------------
>
>Message: 2
>Date: Thu, 29 Nov 2007 19:03:59 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] gmxtest seems to have missing files
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <474EFF0F.8090306 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Amin Astaneh wrote:
>> Hello gmx-users list:
>>
>> I downloaded the gmxtest tarball to test my installation. When I ran it,
>> I get these errors:
>probably meant that you haven't run source GMXRC
>test it using the command:
>luck
>
>>
>> 69:0 gmxtest # ./gmxtest.pl simple
>> No topol.tpr file in angles1. grompp failed
>> FAILED. Check files in angles1
>> No topol.tpr file in angles125. grompp failed
>> FAILED. Check files in angles125
>> No topol.tpr file in bham. grompp failed
>> FAILED. Check files in bham
>> ...
>>
>> It seems that the test suite requires a topol.tpr file in each test case
>> directory. There are none.
>>
>> Thank you for your time.
>>
>> Amin Astaneh
>> USF Research Computing
>> http://rc.usf.edu
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>--
>David van der Spoel, Ph.D.
>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 29 Nov 2007 13:13:48 -0500
>From: chris.neale at utoronto.ca
>Subject: [gmx-users] osmotic pressure in Gromacs
>To: gmx-users at gromacs.org
>Message-ID: <20071129131348.mv65nikthcwg4k80 at webmail.utoronto.ca>
>Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
>> We want to simulate water transport through channel by osmotic
>> pressurce using Gromacs software. The force on the water molecules
>> is usually applied only in a buffer zone, not on all water
>> molecules. How to set up my system. In my opion, we can only define
>> a simple group by index. Water molecules are moving, so the water
>> molecules in a buffer zone change frequently. How to define the
>> group of water molecules in a buffer zone. Gromacs can do it?
>> thanks!
>
>First: what is a 'buffer zone'? And why do you need one? Also, you
>should be able to model osmotic pressure with the application of
>special forces, no?
>
>Perhaps I entirely missed the point. If not, here is what came to mind.
>
>One admitedly strange way to apply forces based on position would be
>to run gromacs in very short segments using the pull code to apply the
>forces and every time you stop gromacs run your own scripts or gromacs
>utilities to determine which waters should be feeling your force and
>make a new .ndx file to cause that to happen in the next mrdun
>segment. You should then determine how long to run your segments based
>on the diffusion of normal water and take an average of how long it
>before recalculating. I figure 0.4A^2/ps diffusion suggests segments
>of < 10ps (but don't take my word for it) making this a very time
>consuming endeavour.
>
>Also not that this method would destroy dynamics information about the waters.
>
>
>
>
>
>------------------------------
>
>Message: 4
>Date: Thu, 29 Nov 2007 19:29:57 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Double precision test failure
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <474F0525.2090904 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Chris Snook wrote:
>> I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2
>> Duo processor.
>>
>> I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and
>> run the test program. The single precision tests run OK. But the double
>> precision tests completely fail with the following output (partial):
>>
>> No topol.tpr file in angles1. grompp failed
>> FAILED. Check files in angles1
>> No topol.tpr file in angles125. grompp failed
>> FAILED. Check files in angles125
>> No topol.tpr file in bham. grompp failed
>> FAILED. Check files in bham
>> etc
>> No topol.tpr file in kernel334. grompp failed
>> FAILED. Check files in kernel334
>> 63 out of 63 kernel tests FAILED
>> readline() on closed filehandle PIPE at ./gmxtest.pl line 353.
>> etc
>>
>> I've checked the archives and the manual and haven't seen anything relevant to
>> this. Any help would be appreciated.
>
>did you source GMXRC?
>>
>> Regards
>>
>> Chris
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>--
>David van der Spoel, Ph.D.
>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
>------------------------------
>
>Message: 5
>Date: Thu, 29 Nov 2007 12:17:56 -0800 (PST)
>From: "özge" "kül" <ozgekul8233 at yahoo.com>
>Subject: Re: [gmx-users] rtp file
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <132118.42313.qm at web56401.mail.re3.yahoo.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Thank you Justin A. Lemkul for your interest of my question.I looked at my 4htc.pdb file but I saw that LPD1 MET11.I don't understand why it ends with that fatal error.I thougth that my pdb structure had wrong structure and then I looked it up in the sybyl program.I saw LPD1 lone pair there.Anyone has an idea?
>
> Thank you very much
> Özge Kül
>Hacettepe University
> Chemistry Department
>"Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> Quoting özge kül :
>
>> Hi all,
>>
>> I try to use gromacs for my callculations of thrombin structure.I obtained
>> the pdb from protein databank.But the structure has some missing residues at
>> the end of the chain and et the beginning of the chain.I completed the
>> residues with sybyl 7.3.And then I started to my simulation.But in the
>> pdb2gmx command I got this
>>
>> fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms.
>
>That means the residue has atoms that are named differently than those in the
>.rtp file. If the atom does indeed belong, determine what it is and rename it
>in the .pdb file, not the .rtp.
>
>>
>> Then I looked at the .rtp file.I want to learn how can I add a missing
>> thing to the .rtp file.I search for the list that have the same titile.But
>> one of you please write me how can I do this.My simulation is depend on this
>> fatal error.
>
>You should not make changes to the .rtp file unless you absolutely know what
>you're doing.
>
>-Justin
>
>>
>> Thank you very much
>> Özge Kül
>>
>> Hacettepe University
>> Chemistry Department
>>
>>
>> ---------------------------------
>> Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it
>> now.
>
>
>
>========================================
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul at vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
>========================================
>_______________________________________________
>gmx-users mailing list gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>---------------------------------
>Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now.
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>------------------------------
>
>Message: 6
>Date: Thu, 29 Nov 2007 15:29:28 -0500
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] rtp file
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1196368168.474f212806d07 at webmail.vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Quoting özge kül <ozgekul8233 at yahoo.com>:
>
>> Thank you Justin A. Lemkul for your interest of my question.I looked at my
>> 4htc.pdb file but I saw that LPD1 MET11.I don't understand why it ends with
>> that fatal error.I thougth that my pdb structure had wrong structure and then
>> I looked it up in the sybyl program.I saw LPD1 lone pair there.Anyone has an
>> idea?
>
>The program ends in a fatal error because there is in fact no atom called LPD1
>within a methionine residue, as far as the force field (and most standard
>nomenclature) is concerned. Read the error message: "atom LPD1 not found." If
>LPD1 is a lone pair, as you claim, than it is obviously not an atom, and hence
>why pdb2gmx is complaining. Is this residue something you modified in Sybyl?
>Because I can't find anything in 4htc.pdb that says LPD1.
>
>-Justin
>
>>
>> Thank you very much
>> Özge Kül
>> Hacettepe University
>> Chemistry Department
>> "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>> Quoting özge kül :
>>
>> > Hi all,
>> >
>> > I try to use gromacs for my callculations of thrombin structure.I obtained
>> > the pdb from protein databank.But the structure has some missing residues
>> at
>> > the end of the chain and et the beginning of the chain.I completed the
>> > residues with sybyl 7.3.And then I started to my simulation.But in the
>> > pdb2gmx command I got this
>> >
>> > fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms.
>>
>> That means the residue has atoms that are named differently than those in the
>> .rtp file. If the atom does indeed belong, determine what it is and rename it
>> in the .pdb file, not the .rtp.
>>
>> >
>> > Then I looked at the .rtp file.I want to learn how can I add a missing
>> > thing to the .rtp file.I search for the list that have the same titile.But
>> > one of you please write me how can I do this.My simulation is depend on
>> this
>> > fatal error.
>>
>> You should not make changes to the .rtp file unless you absolutely know what
>> you're doing.
>>
>> -Justin
>>
>> >
>> > Thank you very much
>> > Özge Kül
>> >
>> > Hacettepe University
>> > Chemistry Department
>> >
>> >
>> > ---------------------------------
>> > Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it
>> > now.
>>
>>
>>
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> ---------------------------------
>> Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it
>> now.
>
>
>
>========================================
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul at vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
>========================================
>
>
>------------------------------
>
>Message: 7
>Date: Thu, 29 Nov 2007 16:35:00 -0500
>From: Chris Snook <snookc at musc.edu>
>Subject: Re: [gmx-users] Double precision test failure
>To: gmx-users at gromacs.org
>Message-ID: <20071129163500.huvpwme8n4woo8o4 at webmail.musc.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format="flowed"
>
>Yes,
>
>The paths for GMXBIN, GMXLDLIB, GMXDATA and GMXMAN are correctly
>defined whether
>I use sh or bash as the shell. I do get the following errors when I run
>GMXRC in
>either shell:
>
>../bin/GMXRC: line 35: return: can only `return' from a function or sourced
>script
>../bin/GMXRC: line 44: CSH:: command not found
>../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near
>unexpected token `setenv'
>../bin/GMXRC: /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (!
>$?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'
>
>Regards
>
>Chris
>
>Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>
>> Chris Snook wrote:
>>> I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel
>>> 2.16GHz Core 2
>>> Duo processor.
>>>
>>> I have downloaded and installed the v 3.3.2 binaries of gromacs for
>>> this OS and
>>> run the test program. The single precision tests run OK. But the double
>>> precision tests completely fail with the following output (partial):
>>>
>>> No topol.tpr file in angles1. grompp failed
>>> FAILED. Check files in angles1
>>> No topol.tpr file in angles125. grompp failed
>>> FAILED. Check files in angles125
>>> No topol.tpr file in bham. grompp failed
>>> FAILED. Check files in bham
>>> etc
>>> No topol.tpr file in kernel334. grompp failed
>>> FAILED. Check files in kernel334
>>> 63 out of 63 kernel tests FAILED
>>> readline() on closed filehandle PIPE at ./gmxtest.pl line 353.
>>> etc
>>>
>>> I've checked the archives and the manual and haven't seen anything
>>> relevant to
>>> this. Any help would be appreciated.
>>
>> did you source GMXRC?
>>>
>>> Regards
>>>
>>> Chris
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> --
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
>
>
>
>------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>
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