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
Received on Mon Feb 14 2011 - 19:30:05 PST
