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
Received on Mon Feb 14 2011 - 18:00:04 PST
