Thank you Jason,
> su root
> Yikes. Don't do this. Change the ownership of AMBERHOME and install as
> a regular user instead.
I use root because I want install it for all users can use it.
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.
I try to re-run it use gnu,
Configure completed!
./congigure gnu
but "make install" failed, get the following error:
may be I miss some thing?
I note this message,
> /home/mabiao/amber12/lib/libfftw3.a(vrank3-transpose.o)
> :vrank3-transpose.c:(.text+0x1155): more undefined references to
> `_intel_fast_memcpy' follow
is this necessary to remove the old compiled files, if necessary does amber
has some script to clean this files?
for reference I attached my bashrc file.
thanks for your attention.
Biao
== Error Info from here =============================================
(this is only the part of end block)
…
/home/mabiao/amber12/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1155):
more undefined references to `_intel_fast_memcpy' follow
/home/mabiao/amber12/lib/libfftw3.a(dht-rader.o): In function `apply':
dht-rader.c:(.text+0xf4): undefined reference to `_intel_fast_memset'
/home/mabiao/amber12/lib/libfftw3.a(dht-rader.o): In function `awake':
dht-rader.c:(.text+0x86a): undefined reference to `_intel_fast_memset'
/home/mabiao/amber12/lib/libfftw3.a(rank0.o): In function `apply_memcpy':
rank0.c:(.text+0x5f0): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(rank0.o): In function
`apply_memcpy_loop':
rank0.c:(.text+0x739): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(rank0.o): In function `memcpy_loop':
rank0.c:(.text+0x857): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(cpy1d.o): In function `fftw_cpy1d':
cpy1d.c:(.text+0xf8): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(trig.o): In function `cexpl_sincos':
trig.c:(.text+0x18d): undefined reference to `__libm_sse2_sincos'
/home/mabiao/amber12/lib/libfftw3.a(trig.o): In function `fftw_mktriggen':
trig.c:(.text+0x440): undefined reference to `__libm_sse2_sincos'
trig.c:(.text+0x551): undefined reference to `__libm_sse2_sincos'
/home/mabiao/amber12/lib/libfftw3.a(cpy2d.o): In function `fftw_cpy2d':
cpy2d.c:(.text+0x629): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(cpy2d.o): In function `fftw_cpy2d_ci':
cpy2d.c:(.text+0xe15): undefined reference to `_intel_fast_memcpy'
cpy2d.c:(.text+0x14a8): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(cpy2d.o): In function `fftw_cpy2d_co':
cpy2d.c:(.text+0x1da5): undefined reference to `_intel_fast_memcpy'
cpy2d.c:(.text+0x2438): undefined reference to `_intel_fast_memcpy'
/home/mabiao/amber12/lib/libfftw3.a(cpy2d.o):cpy2d.c:(.text+0x2c71): more
undefined references to `_intel_fast_memcpy' follow
collect2: error: ld returned 1 exit status
make[2]: *** [pbsa] Error 1
make[2]: Leaving directory `/home/mabiao/amber12/AmberTools/src/pbsa'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/home/mabiao/amber12/AmberTools/src'
make: *** [install] Error 2
On Wed, May 14, 2014 at 11:48 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 14 2014 - 20:00:02 PDT
