Re: [gmx-users] Installing gromacs from git
Hi, if you configure the git version without the --enable-mpi flag, it will turn on threads by default. Depending on the number of processors you have on your workstation, it will then use these many threads. You can disable that with mdrun -nt 1 ... Carsten On Jul 10, 2010, at 1:57 AM, Sai Pooja wrote: Hi, I had used the following steps to install a git version of gromacs. It installed correctly and I have been using it for a while. However, even though I didnt install the parallel version, when I use mdrun it runs in parallel. Is installation in the parallel mode by default? Is there a way to use it without parallelization? 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install Pooja On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use make links?* Do you normally make links? If so, you'll be over-writing the executables in /usr/local/bin. One other possible side effect is that if both /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't define which executable to use unambiguously without specifying the whole path name for each executable. If you're using several version of Gromacs concurrently on the same machine, it's probably best to just install them in their own locations and source the proper GMXRC when you log in to use the version you want. -Justin * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while
Re: [gmx-users] Installing gromacs from git
Hi, I had used the following steps to install a git version of gromacs. It installed correctly and I have been using it for a while. However, even though I didnt install the parallel version, when I use mdrun it runs in parallel. Is installation in the parallel mode by default? Is there a way to use it without parallelization? 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install Pooja On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use make links?* Do you normally make links? If so, you'll be over-writing the executables in /usr/local/bin. One other possible side effect is that if both /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't define which executable to use unambiguously without specifying the whole path name for each executable. If you're using several version of Gromacs concurrently on the same machine, it's probably best to just install them in their own locations and source the proper GMXRC when you log in to use the version you want. -Justin * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja saipo...@gmail.com mailto: saipo...@gmail.com wrote: I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install
Re: [gmx-users] Installing gromacs from git
I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 This is just make cleaning up after recursive invocation. The actual error is further up. Note that if configure failed according to your previous email, then there's no point to using make. Mark On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 9:35 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org I am sorry that was a typo in the mail. It was set to lib That makes it hard for us to have confidence in the rest of your command lines - copying and pasting the results of history is a good way to avoid such problems. As such I can only suggest looking for error in the last 100 lines of config.log and seeing what you find. That, and trying it all again :-) Mark On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul jalem...@vt.eduwrote: Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman
Re: [gmx-users] Installing gromacs from git
For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use make links?* * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja saipo...@gmail.com wrote: I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 This is just make cleaning up after recursive invocation. The actual error is further up. Note that if configure failed according to your previous email, then there's no point to using make. Mark On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 9:35 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org I am sorry that was a typo in the mail. It was set to lib That makes it hard for us to have confidence in the rest of your command lines - copying and pasting the results of history is a good way to avoid such problems. As such I can only suggest looking for error in the last 100 lines of config.log and seeing what you find. That, and trying it all again :-) Mark On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul jalem...@vt.eduwrote: Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin
Re: [gmx-users] Installing gromacs from git
Sai Pooja wrote: For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use make links?* Do you normally make links? If so, you'll be over-writing the executables in /usr/local/bin. One other possible side effect is that if both /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't define which executable to use unambiguously without specifying the whole path name for each executable. If you're using several version of Gromacs concurrently on the same machine, it's probably best to just install them in their own locations and source the proper GMXRC when you log in to use the version you want. -Justin * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 This is just make cleaning up after recursive invocation. The actual error is further up. Note that if configure failed according to your previous email, then there's no point to using make. Mark On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 9:35 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org I am sorry that was a typo in the mail. It was set to lib
[gmx-users] Installing gromacs from git
Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
I am sorry that was a typo in the mail. It was set to lib On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
- Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 9:35 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org I am sorry that was a typo in the mail. It was set to lib That makes it hard for us to have confidence in the rest of your command lines - copying and pasting the results of history is a good way to avoid such problems. As such I can only suggest looking for error in the last 100 lines of config.log and seeing what you find. That, and trying it all again :-) Mark On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 Pooja On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 9:35 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org I am sorry that was a typo in the mail. It was set to lib That makes it hard for us to have confidence in the rest of your command lines - copying and pasting the results of history is a good way to avoid such problems. As such I can only suggest looking for error in the last 100 lines of config.log and seeing what you find. That, and trying it all again :-) Mark On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul jalem...@vt.eduwrote: Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
- Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd ..194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 This is just make cleaning up after recursive invocation. The actual error is further up. Note that if configure failed according to your previous email, then there's no point to using make. Mark On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com Date: Sunday, June 20, 2010 9:35 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org I am sorry that was a typo in the mail. It was set to lib That makes it hard for us to have confidence in the rest of your command lines - copying and pasting the results of history is a good way to avoid such problems. As such I can only suggest looking for error in the last 100 lines of config.log and seeing what you find. That, and trying it all again :-) Mark On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Hi, I followed the following steps to install gromacs from the git repository: 1) installed git 2) got a clone of gromacs using the anonymous option 3) installed fftw libraries using ./configure --enable-float --prefix=/fs/home/sm868 make make install 4)export CPPFLAGS=-I/fs/home/sm868/include export LDFLAGS=-L/fs/home/sm868/include 6)ran ./bootstrap 7)ran ./configure --prefix=/fs/home/sm868 8)I get the error - checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory. -Justin Can someone help me with this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
