Re: [gmx-users] Installation of gromacs 4.5.4 on windows using cygwin

Looks like you are compiling 4.5.1. You should try compiling the latest version in the 4.5 series, 4.5.7. -- Szilárd On Sun, Sep 15, 2013 at 6:39 PM, Muthukumaran R wrote: > hello, > > I am trying to install gromacs in cygwin but after issuing "make", > installation stops with the following erro

[gmx-users] Installation of gromacs 4.5.4 on windows using cygwin

hello, I am trying to install gromacs in cygwin but after issuing "make", installation stops with the following error Makefile:1315: recipe for target `gmx_tune_pme.lo' failed make[3]: *** [gmx_tune_pme.lo] Error 1 make[3]: Leaving directory `/usr/local/gromacs-4.5.1/src/tools' Makefile:301: reci

Re: Fw: [gmx-users] Installation of GROMACS on server

*From:* Anirban *To:* Shima Arasteh ; Discussion list for GROMACS users *Sent:* Tuesday, May 22, 2012 1:33 PM *Subject:* Re: [gmx-users] Installation of GROMACS on server On Tue, May 22, 2012 at 2:17 PM, Shima Arasteh mailto:shima_arasteh2...@yahoo.com>> wrote: De

Fw: [gmx-users] Installation of GROMACS on server

Would you guide me to a link which may help me? Thanks so much.   Sincerely, Shima From: Anirban To: Shima Arasteh ; Discussion list for GROMACS users Sent: Tuesday, May 22, 2012 1:33 PM Subject: Re: [gmx-users] Installation of GROMACS on server On

Re: [gmx-users] Installation of GROMACS on server

On Tue, May 22, 2012 at 2:17 PM, Shima Arasteh wrote: > > Dear gmx users, > If I am not admin of the server, would it be possible that I install the > GROMACS 4.5.5 in my account (user) or upgrade the GROMACS version? > You can install latest version of GROMACS in your local directory by giving

Re: [gmx-users] Installation of GROMACS on server

Yes, it could be possible. You have to install it on your local folder where you have the right permissions. This is specified with the --prefix option on the configure script (if using automake/automake installation) or the corresponding option with cmake (I don't know wich one is it, check th

[gmx-users] Installation of GROMACS on server

 Dear gmx users, If I am not admin of the server, would it be possible that I install the GROMACS 4.5.5 in my account (user) or upgrade the GROMACS version? Thanks for your suggestions in advance. Sincerely, Shima-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mail

Re: [gmx-users] Installation of gromacs-gpu on windows

I think so! 2011/7/8 Szilárd Páll : > I think you made the right decision! :) > -- > Szilárd > > > > On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote: >> Thanks a lot! >> Now we decided to use gromacs under linux and the installation of >> gromacs and gromacs-gpu has passed without errors >>

Re: [gmx-users] Installation of gromacs-gpu on windows

I think you made the right decision! :) -- Szilárd On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар wrote: > Thanks a lot! > Now we decided to use gromacs under linux and the installation of > gromacs and gromacs-gpu has passed without errors > Problem is solved :) > > 2011/7/8 Szilárd Páll : >>

Re: [gmx-users] Installation of gromacs-gpu on windows

Thanks a lot! Now we decided to use gromacs under linux and the installation of gromacs and gromacs-gpu has passed without errors Problem is solved :) 2011/7/8 Szilárd Páll : > Well, unfortunately I don't know of any step-by-step tutorial, but > from what I remember the workflow is pretty straight

Re: [gmx-users] Installation of gromacs-gpu on windows

Well, unfortunately I don't know of any step-by-step tutorial, but from what I remember the workflow is pretty straightforward and looks something like this: - Download dependencies, there is precompiled OpenMM and FFTW for Windows. - Run CMake, you'll have to set up the library dependencies manua

Re: [gmx-users] Installation of gromacs-gpu on windows

Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step com

Re: [gmx-users] Installation of gromacs-gpu on windows

Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are

[gmx-users] Installation of gromacs-gpu on windows

Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs unde

Re: [gmx-users] installation of gromacs

On 17/03/11, Diego Enry wrote: > You got this wrong > export CPPFLAGS="-I/home/local/fftw/include" > export LDFLAGS="-L/home/local/fftw/lib" > > replace by this > export CPPFLAGS="-I$HOME/local/fftw/include" > export LDFLAGS="-L$HOME/local/fftw/lib" > This is immaterial if Thomas installed t

Re: [gmx-users] installation of gromacs

Thomas Koller wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3

Re: [gmx-users] installation of gromacs

You got this wrong export CPPFLAGS="-I/home/local/fftw/include" export LDFLAGS="-L/home/local/fftw/lib" replace by this export CPPFLAGS="-I$HOME/local/fftw/include" export LDFLAGS="-L$HOME/local/fftw/lib" On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller wrote: > Now I get this again: > > checkin

Re: [gmx-users] installation of gromacs

On 17/03/11, Thomas Koller wrote: > Now I get this again: > > checking for fftw3.h... configure: error: Cannot find the default external > FFT library (fftw3). > > > > Please follow my way: > > i) I unpacke fftw and gromacs to two folders. > iii) I go the the fftw folder and make: >    

[gmx-users] installation of gromacs

Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-sh

Re: [gmx-users] installation of gromacs

Hi Thomas, the error you see indeed suggests that something is messed up with your compiler. In your case however I think that is due to the CPPFLAGS and LDFLAGS you set. Those sometimes mess with the configure makros. Try export CPPFLAGS= export LDFLAGS= export LD_LIBRARY_PATH= to erase what yo

Re: [gmx-users] installation of gromacs

On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote: > Hi Nuno, > > I have still problems with the insatllation of the 4.0.7 version. > > After unpacking of fftw and gromacs, I did: > > In the fftw folder: > > ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared > --enable-f

Re: [gmx-users] installation of gromacs

Hi Thomas, please send the complete config.log. After you try what I suggest bellow. I guess the environment variables for compilers and libs are not set correctly, not your fault, we'll check on the config file. #make sure your're usnig bash bash #export the regular variables export CPPFLAGS="-

[gmx-users] installation of gromacs

Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS="-I$HOME/local/fftw3/include" expor

Re: [gmx-users] installation of gromacs

On 16/03/11, Thomas Koller wrote: > Hello, > > I did the procedure as described, but at the end of the configuration of > gromacs, I obtain this message: > > checking size of void*... configure: error: cannot compute sizeof (void*) > See `config.log' for more details. > > What is the proble

[gmx-users] installation of gromacs

Hello, I did the procedure as described, but at the end of the configuration of gromacs, I obtain this message: checking size of void*... configure: error: cannot compute sizeof (void*) See `config.log' for more details. What is the problem? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freu

Re: [gmx-users] installation of gromacs

Hello, it seems FFTW3 is not installed in the LD_LIBRARY_PATH and/or the fftw3 headers can not be found. On Ubuntu, most likely the headers are not installed (available in the package libfftw3-dev). However it is really easy to compile FFTW3 yourself and install it inside your $HOME. Then you do n

Re: [gmx-users] installation of gromacs

The most basic question is: did you install FFTW as root or superuser ? sudo make install If so, try to provide fftw /lib and /include locations (using CPPFLAGS and LDFLAGS) while configuring GMX. (from the Installation Instructions) setenv CPPFLAGS -I/home/joe/fftw/include setenv LDFLAGS -L/ho

[gmx-users] installation of gromacs

Hello, I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 3.2.2 and did as in the instructions: ./configure --enable-float make make install After that I ran: ./configure with Gromacs, but I always get: checking for fftw3.h... configure: error: Cannot find the defau

Re: [gmx-users] installation of gromacs on windows using cygwin

On 5/11/2010 10:48 PM, bharat gupta wrote: I followed the same instructions given in the gromacs manual , step by step ... I first tried installing gromacs with the first command given in the manual and then again I installed with the options for FLAGS but finally ended up with the following er

Re: [gmx-users] installation of gromacs on windows using cygwin

bharat gupta wrote: I think I was installing the linux version of fftw3 on windows .. I downloaded this file - fftw-3.2.2.pl1-dll32.zip for installation .. but ./configure command is not working for this file ... as I am getting the fol

Re: [gmx-users] installation of gromacs on windows using cygwin

I think I was installing the linux version of fftw3 on windows .. I downloaded this file - fftw-3.2.2.pl1-dll32.zip for installation .. but ./configure command is not working for this file ... as I am getting the following error $ ./configure

Re: [gmx-users] installation of gromacs on windows using cygwin

I followed the same instructions given in the gromacs manual , step by step ... I first tried installing gromacs with the first command given in the manual and then again I installed with the options for FLAGS but finally ended up with the following error in both the above mentioned conditions :-

Re: [gmx-users] installation of gromacs on windows using cygwin

On 5/11/2010 6:30 PM, bharat gupta wrote: Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be locat

Re: [gmx-users] installation of gromacs on windows using cygwin

Hi, If you have installed fftw3 in the standard location it whould work out of the box. Otherwise, you have to set the LDFLAGS and CPPFLAGS to the library and include location respectively. However, there's one more thing I can think of: did you make sure that you compiled fftw3 in single precisi

[gmx-users] installation of gromacs on windows using cygwin

Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be located .. can anybody pls help find out where am I

Re: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

On Tue, 5 Oct 2010 20:03:41 +0530 (IST) ras...@chem.iitb.ac.in wrote: > Hi All, > > I want to install Gromacs 4.5.1 version on a cluster system (high > performance computing facility) in our institute. I don't have access > to root and thus, I have to install gromacs in my home directory. > > Th

RE: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

are not 100% sure, but version 4.5.1 probably works fine with gcc 4.1.2. Berk > Date: Tue, 5 Oct 2010 20:03:41 +0530 > From: ras...@chem.iitb.ac.in > To: gmx-users@gromacs.org > Subject: [gmx-users] Installation of gromacs on a cluster with gcc version > 4.1.2 > > Hi All, &

[gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

Hi All, I want to install Gromacs 4.5.1 version on a cluster system (high performance computing facility) in our institute. I don't have access to root and thus, I have to install gromacs in my home directory. The problem is that, the cluster has CentOS 5.4 as the operating system and the gcc ver

Re: [gmx-users] Installation of gromacs 4.0.5 on a Mac

Thanks, It works, I had to create the .bash_profile with the line "source /usr/ local/gromacs/bin/GMXRC On Jul 13, 2009, at 10:47 PM, Justin A. Lemkul wrote: Gunnar Widtfeldt wrote: I couldn't find the shell configuration file so I created a file called .tschrc in my home folder with the

Re: [gmx-users] Installation of gromacs 4.0.5 on a Mac

Gunnar Widtfeldt wrote: I couldn't find the shell configuration file so I created a file called .tschrc in my home folder with the line "source /usr/local/gromacs/bin/GMXRC Right, because you need to add it - the location of Gromacs is not a standard location. If you're on a Mac running 1

Re: [gmx-users] Installation of gromacs 4.0.5 on a Mac

Gunnar Widtfeldt wrote: I couldn't find the shell configuration file so I created a file called .tschrc in my home folder with the line "source /usr/local/gromacs/bin/GMXRC That didn't do it. Again I am new to unix commands. Try typing it on the command line or open a new terminal. Maybe th

Re: [gmx-users] Installation of gromacs 4.0.5 on a Mac

I couldn't find the shell configuration file so I created a file called .tschrc in my home folder with the line "source /usr/local/ gromacs/bin/GMXRC That didn't do it. Again I am new to unix commands. On Jul 13, 2009, at 10:24 PM, Justin A. Lemkul wrote: Gunnar Widtfeldt wrote: HI. I h

Re: [gmx-users] Installation of gromacs 4.0.5 on a Mac

Gunnar Widtfeldt wrote: HI. I have compiled and installed gromacs 4.0.5 on a mac running 10.5. I have also installed fftw-3.2.1 gsl-1.11 openmotif-2.3.1 and openmpi-1.2.8 Now, I think everything went fine with the installation (I didn't spot any terrible warning or errors) but since I'm new

[gmx-users] Installation of gromacs 4.0.5 on a Mac

HI. I have compiled and installed gromacs 4.0.5 on a mac running 10.5. I have also installed fftw-3.2.1 gsl-1.11 openmotif-2.3.1 and openmpi-1.2.8 Now, I think everything went fine with the installation (I didn't spot any terrible warning or errors) but since I'm new to unix commands I'm

Re: Re: Re: [gmx-users] Installation of Gromacs and speed...

> Thank you for the reply. I have some more queries: > So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? Maybe... depends if there were any meaningful speed-ups in parts of the code you actually use. > Do you suggest me to update the Gromacs versions on both the systems to > Gr

Re: [gmx-users] Installation of Gromacs and speed...

TED]> To: [EMAIL PROTECTED] Date: Fri, 5 Jan 2007 08:26:29 + (GMT) Subject: [gmx-users] Installation of Gromacs and speed... sharada, it is better to load new version and uninstall the older version. you have to load new fftw.

Re: Re: Re: [gmx-users] Installation of Gromacs and speed...

Thank you for the reply. I have some more queries: So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? Do you suggest me to update the Gromacs versions on both the systems to Gromacs 3.3.1? For this do I have to remove the older versions ? Will it ov

Re: [gmx-users] Installation of GROMACS

Hello, I had the same problem (under fedora core 5 on a VMWare workstation) and solved it by deleting the natively installed fftw package and reinstall it using a rpm found on the web. Seb. Ansgar Esztermann a écrit : On Tue, Nov 28, 2006 at 08:59:42AM -0500, Mark Zottola wrote: I am

Re: [gmx-users] Installation of GROMACS

On Tue, Nov 28, 2006 at 08:59:42AM -0500, Mark Zottola wrote: > I am trying to install GROMACS 3.3-1. the issue is that it is looking for > the libfftw3f.so.3 file. This file exists in /usr/lib. However, the rpm > install does not see this. I cannot find a way to see tha path that the rpm > wan

[gmx-users] Installation of GROMACS

I am trying to install GROMACS 3.3-1. the issue is that it is looking for the libfftw3f.so.3 file. This file exists in /usr/lib. However, the rpm install does not see this. I cannot find a way to see tha path that the rpm wants to detect this file. Can anyone tell me where this library file s

Re: [gmx-users] Installation of Gromacs into BG/L

Dear Florian, Thanks for your help. It worked! I should have tried fftw-3.1.2 first ... Best wishes, > hi, > > On Wednesday 20 September 2006 16:07, Hiroshi Fujisaki wrote: > > Dear Gromacs users, > > > > I am now trying to install gromacs into our BlueGene facility, > > but I fail when I do ma

Re: [gmx-users] Installation of Gromacs into BG/L

hi, On Wednesday 20 September 2006 16:07, Hiroshi Fujisaki wrote: > Dear Gromacs users, > > I am now trying to install gromacs into our BlueGene facility, > but I fail when I do make. (configure seems to be fine.) > The link to the FFTW library does not seem to work. > I use fftw-2.1.5. I attach t

[gmx-users] Installation of Gromacs into BG/L

Dear Gromacs users, I am now trying to install gromacs into our BlueGene facility, but I fail when I do make. (configure seems to be fine.) The link to the FFTW library does not seem to work. I use fftw-2.1.5. I attach the excerpt of the make log file here (the last part of the log). #