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
Received on Mon Feb 14 2011 - 19:00:08 PST
