On Wed, 2014-05-14 at 23:24 +0900, Biao Ma wrote:
> Thanks Junjun and Dan,
>
> Today, I try to update AmberTools,
>
> first, I do the following work, I got some error when run ./update_amber
> --check-updates.
> I think that no effect on next process, and I did the next process,
> to run "# ./update_amber -update" and type "Yes" to download the update
> files.
> then, I try to re-run " ./configure intel", but failed the error info is
> following.
>
> who can tell me is where wrong?
>
> thank you,
> Biao
>
> ==================
>
> cd $AMBERHOME
>
> su root
Yikes. Don't do this. Change the ownership of AMBERHOME and install as
a regular user instead.
>
> ./update_amber -v
>
> Version is reported as <version>.<patches applied>
>
> AmberTools version 13.00
>
> Amber version 12.15
>
> ./update_amber --check-updates
>
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 13 patches:
>
> update.1, update.2, update.3, update.4, update.5, update.6, update.7,
> update.8, update.9, update.10,
>
> update.11, update.12, update.13, update.14, update.15, update.16,
> update.17, update.18, update.19, update.20,
>
> update.21, update.22, update.23, update.24
>
> Traceback (most recent call last):
>
> File "./update_amber", line 23, in <module>
>
> app.mainloop()
>
> File "/usr/local/amber12/updateutils/main.py", line 467, in mainloop
>
> self.check_updates()
>
> File "/usr/local/amber12/updateutils/main.py", line 175, in check_updates
>
> self.verbose) + '\n')
>
> File "/usr/local/amber12/updateutils/repos.py", line 185, in patch_details
>
> return PatchRepository.patch_details(self, first, verbose)
>
> File "/usr/local/amber12/updateutils/repos.py", line 59, in patch_details
>
> progs = self.patch_list.programs(i)
>
> File "/usr/local/amber12/updateutils/patchlist.py", line 237, in programs
>
> return self._info_wrapper(idx, 'programs')
>
> File "/usr/local/amber12/updateutils/patchlist.py", line 355, in
> _info_wrapper
>
> return getattr(self._instantiate(idx), attr)()
>
> File "/usr/local/amber12/updateutils/downloader.py", line 98, in new_fcn
>
> return fcn(*args, **kwargs)
>
> File "/usr/local/amber12/updateutils/patchlist.py", line 337, in
> _instantiate
>
> self.sizere.findall(urlopen(self.names[idx]).info())[0])
>
> TypeError: expected string or buffer
This was fixed by one of the first AmberTools 13 updates, and only hit
you because you had already applied most Amber updates. AmberTools 14
(the recommended version) does not have this problem.
>
>
> =======================================
>
> # ./configure intel
> Checking for updates... Checking for available patches online. This may
> take a few seconds... Available AmberTools 13 patches: update.1, update.2,
> update.3, update.4, update.5, update.6, update.7, update.8, update.9,
> update.10, update.11, update.12, update.13, update.14, update.15,
> update.16, update.17, update.18, update.19, update.20, update.21,
> update.22, update.23, update.24 Traceback (most recent call last): File
> "./update_amber", line 23, in <module> app.mainloop() File
> "/usr/local/amber12/updateutils/main.py", line 467, in mainloop
> self.check_updates() File "/usr/local/amber12/updateutils/main.py", line
> 175, in check_updates self.verbose) + '\n') File
> "/usr/local/amber12/updateutils/repos.py", line 185, in patch_details
> return PatchRepository.patch_details(self, first, verbose) File
> "/usr/local/amber12/updateutils/repos.py", line 59, in patch_details progs
> = self.patch_list.programs(i) File
> "/usr/local/amber12/updateutils/patchlist.py", line 237, in programs return
> self._info_wrapper(idx, 'programs') File
> "/usr/local/amber12/updateutils/patchlist.py", line 355, in _info_wrapper
> return getattr(self._instantiate(idx), attr)() File
> "/usr/local/amber12/updateutils/downloader.py", line 98, in new_fcn return
> fcn(*args, **kwargs) File "/usr/local/amber12/updateutils/patchlist.py",
> line 337, in _instantiate
> self.sizere.findall(urlopen(self.names[idx]).info())[0]) TypeError:
> expected string or buffer Check for updates failed. Detected icc version 11
> Detected ifort version 11 Testing the icc compiler: icc
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c OK Testing the
> ifort compiler: ifort -O0 -o testp testp.f OK Testing mixed C/Fortran
> compilation: icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c ifort -O0 -c -o testp.f.o testp.f icc -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o
> -L/opt/intel/Compiler/11.1/080/lib/intel64 -lifport -lifcore -lsvml ld:
> warning: libimf.so, needed by
> /opt/intel/Compiler/11.1/080/lib/intel64/libifport.so.5, not found (try
> using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by
> /opt/intel/Compiler/11.1/080/lib/intel64/libifport.so.5, not found (try
> using -rpath or -rpath-link) ld: testp: hidden symbol
> `__intel_cpu_indicator_init' in
> /opt/intel/Compiler/11.1/080/lib/intel64/libirc.a(cpu_disp.o) is referenced
> by DSO ld: final link failed: Nonrepresentable section on output
> ./configure2: line 1786: ./testp: No such file or directory Error: Unable
> to compile mixed C/Fortran code. Please check your compiler settings and
> configure flags. Configure failed due to the errors above!
Looks like your intel compilers are broken (or your environment is not
set up correctly). You either have to fix your compilers or use GNU
instead.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 14 2014 - 08:00:04 PDT
