I sent numerous responses regarding the errors you were seeing -- including
fixing the error of missing yacc.
See this page
http://ambermd.org/ubuntu.html, which I put in one of my
emails and Professor Case alluded to in his email as well. All packages
listed here are needed to install amber completely.
Professor Case also offered good advice in terms of trying to make use of
error messages provided to you and trying to fix your own issues. The error
messages together with Google is almost always all you need to solve a
particular problem and will help you advance your project far more quickly
than waiting for a mailing list to respond with suggestions on all your
issues.
Many issues you have will probably also have come up in the past, so you can
try looking through the archives to find answers to your problems. For
instance, searching for the first error message in your first post gives the
result
http://archive.ambermd.org/200901/0132.html
which details the answer. Likewise for additional errors.
Good luck,
Jason
2011/2/14 gromacs <ptf1242.163.com>
> tleap probably did not compile because the compile process was
> interrupted above due to the lack of the x11-devel package.
>
> The reason may be above. But how can i solve? If i install xorg-dev
> package, there will be error; However if i did not install xorg-dev, i
> cannot pass the test of tleap.
>
>
> Please if possible give a detailed inforamtion on how to install. Because
> there are too many small errors.
>
>
>
>
>
>
>
>
>
> At 2011-02-15 10:47:17，gromacs <ptf1242.163.com> wrote:
>
> >2) Use sudo -E instead of sudo (sudo -E make test.serial) to make the root
> >shell inherit the environment of the calling session.
> >
> >i used the above method, and still error,
> >
> >cd leap; ./Run.tleap
> >Error: ./tleap -> ../../exe/teLeap does not exist
> >make: *** [test.leap] Error 1
> >
> >
> >If Use the 1) DON'T use sudo to run the test suite
> >I can not run test. Permission denied.
> >
> >
> >So many unexpected error during the install process.
> >
> >Why not put a instruction on these process?
> >
> >
> >
> >
> >
> >
> >At 2011-02-15 09:53:13，"Jason Swails" <jason.swails.gmail.com> wrote:
> >
> >>Do you use "sudo make test.serial"? I'm guessing you do since you've
> >>installed in /usr/local/amber9. This can cause permission issues if you
> >>haven't changed ownership of the directory to your username.
> >>
> >>By default, root shell sessions launched by sudo do not inherit the
> >>environment variables of the shell from which you launched it. That is,
> if
> >>you set AMBERHOME in your current shell (via "export
> >>AMBERHOME=/usr/local/amber9") then use "sudo make test.serial", AMBERHOME
> >>will not be set in that shell session, giving rise to the error you see.
> >>
> >>There are 2 ways around this.
> >>
> >>1) Change ownership of /usr/local/amber9 to your username (sudo chown
> >>`whoami` /usr/local/amber9) and DON'T use sudo to run the test suite
> >>
> >>2) Use sudo -E instead of sudo (sudo -E make test.serial) to make the
> root
> >>shell inherit the environment of the calling session.
> >>
> >>Good luck,
> >>Jason
> >>
> >>2011/2/14 gromacs <ptf1242.163.com>
> >>
> >>> Hi Jason,
> >>>
> >>> I have defined AMBERHOME and the AMBERHOME="usr/local/amber9"
> >>>
> >>> All the test were all right
> >>> But at the final stage,
> >>>
> >>> cd leap; ./Run.tleap
> >>> Error - must define AMBERHOME environment variable
> >>> make: *** [test.leap] Error 1
> >>>
> >>> How can i solve this?
> >>>
> >>> Thanks for your teaching
> >>>
> >>>
> >>>
> >>>
> >>> At 2011-02-15 08:42:54，"Jason Swails" <jason.swails.gmail.com> wrote:
> >>>
> >>> >2011/2/14 gromacs <ptf1242.163.com>
> >>> >
> >>> >> The version i install is AMBER 9, not AMBER 10 or AMBER 11. It seems
> >>> AMBER
> >>> >> 9 not need AmberTool, Do i need to still instll AmberTool?
> >>> >>
> >>> >
> >>> >At this point Amber and AmberTools were released as the same package.
> It
> >>> >wasn't until Amber10 that they were separate distributions (and not
> until
> >>> >Amber 11 that they were released with different root directories).
> You do
> >>> >not need to install any later version of AmberTools in order to get
> Amber
> >>> 9
> >>> >to work.
> >>> >
> >>> >
> >>> >>
> >>> >> And If i install AMBER 9, are there still 2 bugfix.all files that
> will
> >>> have
> >>> >> to apply?
> >>> >>
> >>> >
> >>> >No, just the 1 bugfix.all
> >>> >
> >>> >
> >>> >>
> >>> >> I am using Ubuntu, for install AMBER 9 xorg-dev package also need??
> >>> >>
> >>> >
> >>> >For xleap, yes. You can specifically ask for no xleap (with the flag
> >>> -noX11
> >>> >maybe, or something related), which should avoid this error. If you
> want
> >>> to
> >>> >build xleap, then you will need the xorg-dev package:
> >>> >
> >>> >sudo apt-get install xorg-dev
> >>> >
> >>> >
> >>> >>
> >>> >> I download l_fcompxe_ia32_2011.2.137.tgz, and it is the latest
> version.
> >>> But
> >>> >> after i finished, i type 'which ifort', it did not give any
> response.
> >>> >>
> >>> >
> >>> >Most likely you have to source the appropriate ifortvars.sh variable.
> For
> >>> >my machine, ifort is located in
> >>> >/opt/intel/Compiler/11.1/069/bin/ifortvars.sh . I load the proper
> >>> >environment variables by placing the command
> >>> >
> >>> >source /opt/intel/Compiler/11.1/069/bin/ifortvars.sh intel64
> >>> >
> >>> >(or ia32 for 32-bit OSes).
> >>> >
> >>> >After sourcing this file (if you just place it in the .bashrc you will
> >>> >either have to source the .bashrc again or start a new shell to see
> its
> >>> >effects), type "which ifort" and see if it becomes visible.
> >>> >
> >>> >Good luck,
> >>> >Jason
> >>> >
> >>> >
> >>> >>
> >>> >>
> >>> >> Thanks
> >>> >>
> >>> >>
> >>> >>
> >>> >> At 2011-02-14 20:41:27，"Jason Swails" <jason.swails.gmail.com>
> wrote:
> >>> >>
> >>> >> >2011/2/14 gromacs <ptf1242.163.com>
> >>> >> >
> >>> >> >> Hi,
> >>> >> >>
> >>> >> >> WcActCB.c:1450: error: expected declaration specifiers before
> >>> ‘Widget’
> >>> >> >> WcActCB.c:1450: error: expected declaration specifiers before
> >>> ‘XEvent’
> >>> >> >> WcActCB.c:1450: error: expected declaration specifiers before
> >>> ‘Cardinal’
> >>> >> >> WcActCB.c: In function ‘WcDynamicCallbackACT’:
> >>> >> >> WcActCB.c:1452: error: expected declaration specifiers before
> >>> ‘Widget’
> >>> >> >> WcActCB.c:1452: error: expected declaration specifiers before
> >>> ‘XEvent’
> >>> >> >> WcActCB.c:1452: error: expected declaration specifiers before
> >>> ‘Cardinal’
> >>> >> >> WcActCB.c: In function ‘WcRegisterWcActions’:
> >>> >> >> WcActCB.c:1461: error: expected declaration specifiers before
> >>> >> >> ‘XtAppContext’
> >>> >> >> WcActCB.c:1463: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> >>> ‘__attribute__’
> >>> >> >> before ‘WcActions’
> >>> >> >> WcActCB.c:1463: error: ‘WcActions’ undeclared (first use in this
> >>> >> function)
> >>> >> >> WcActCB.c:1463: error: expected expression before ‘]’ token
> >>> >> >> WcActCB.c:1536: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> >>> ‘__attribute__’
> >>> >> >> before ‘already’
> >>> >> >> WcActCB.c:1536: error: ‘already’ undeclared (first use in this
> >>> function)
> >>> >> >> make[2]: *** [WcActCB.o] Error 1
> >>> >> >> make[2]: Leaving directory
> >>> `/home/uqtpeng1/AMBER/amber9/src/leap/src/Wc'
> >>> >> >> make[1]: *** [install] Error 2
> >>> >> >> make[1]: Leaving directory `/home/uqtpeng1/AMBER/amber9/src/leap'
> >>> >> >> make: *** [serial] Error 2
> >>> >> >>
> >>> >> >> I have gfortran and i installed at different desktops. When 'sudo
> >>> make
> >>> >> >> series', the error will come. WcCreate.h:,
> >>> >> >>
> >>> >> >
> >>> >> >Have you applied all bug fixes to your version of Amber and
> AmberTools
> >>> >> (note
> >>> >> >there will be 2 bugfix.all files that you will have to apply.
> >>> >> >
> >>> >> >
> >>> >> >>
> >>> >> >> How can i solve this problem. I also cannot find a ifort in Inter
> >>> >> website.
> >>> >> >> Even if i download the interfortran from that site, it is not
> easy to
> >>> >> >> install.
> >>> >> >>
> >>> >> >
> >>> >> >Make sure that you have all bug fixes applied and that you have the
> X
> >>> >> >developer package installed:
> >>> >> >
> >>> >> >On new Fedora OS's install the libXt-devel libXext-devel
> >>> >> >libX11-devel libICE-devel libSM-devel packages.
> >>> >> >On old Fedora OS's install the xorg-x11-devel package.
> >>> >> >On RedHat OS's install the XFree86-devel package.
> >>> >> >On Ubuntu OS's install the xorg-dev package.
> >>> >> >For the moment Amber will be configured not to build XLEaP.
> >>> >> >
> >>> >> >As far as installing the intel compiler suite; if you have obtained
> a
> >>> >> >license for it (academic or commercial or whatever), you get an
> >>> installer
> >>> >> >package that you just have to launch and follow the on-screen
> prompts
> >>> (at
> >>> >> >least for versions as recent as 11.1.069).
> >>> >> >
> >>> >> >Good luck!
> >>> >> >Jason
> >>> >> >
> >>> >> >>
> >>> >> >>
> >>> >> >> _______________________________________________
> >>> >> >> AMBER mailing list
> >>> >> >> AMBER.ambermd.org
> >>> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >> >>
> >>> >> >
> >>> >> >
> >>> >> >
> >>> >> >--
> >>> >> >Jason M. Swails
> >>> >> >Quantum Theory Project,
> >>> >> >University of Florida
> >>> >> >Ph.D. Candidate
> >>> >> >352-392-4032
> >>> >> >_______________________________________________
> >>> >> >AMBER mailing list
> >>> >> >AMBER.ambermd.org
> >>> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>> >> _______________________________________________
> >>> >> AMBER mailing list
> >>> >> AMBER.ambermd.org
> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >>
> >>> >
> >>> >
> >>> >
> >>> >--
> >>> >Jason M. Swails
> >>> >Quantum Theory Project,
> >>> >University of Florida
> >>> >Ph.D. Candidate
> >>> >352-392-4032
> >>> >_______________________________________________
> >>> >AMBER mailing list
> >>> >AMBER.ambermd.org
> >>> >http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >>--
> >>Jason M. Swails
> >>Quantum Theory Project,
> >>University of Florida
> >>Ph.D. Candidate
> >>352-392-4032
> >>_______________________________________________
> >>AMBER mailing list
> >>AMBER.ambermd.org
> >>http://lists.ambermd.org/mailman/listinfo/amber
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 14 2011 - 20:00:03 PST
