[AMBER-Developers] AmberTools configure failure and compilation errors

From: Sally Pias <sallypias.gmail.com>
Date: Sun, 11 Apr 2010 00:28:01 -0600

I do not know whether the following issues are important, but I did
not want to neglect reporting them, just in case. If further OS
information is needed, please instruct me how to obtain it, as I'm a
newbie at this sort of thing.

Sally

--
Sally C. Pias
Postdoctoral Associate
Simmerling research group, Stony Brook University
sallypias.gmail.com
==========
A configure failure using intel 10 compilers:
==========
$ arch
x86_64
$ source /opt/intel/fc/10.1.015/bin/ifortvars.sh
$ source /opt/intel/cc/10.1.015/bin/iccvars.sh
$ which icc
/opt/intel/cc/10.1.015/bin/icc
$ which ifort
/opt/intel/fc/10.1.015/bin/ifort
$ cd amber11/AmberTools/src
$ ./configure -static -noX11 intel
Your AMBERHOME environment variable should be set to
/mnt/raidc/sally/ambertools.tabasco/amber11
Testing the icc compiler:
     icc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
ld: skipping incompatible /usr/lib/libm.so when searching for -lm
ld: skipping incompatible /usr/lib/libm.a when searching for -lm
ld: skipping incompatible /usr/bin/../lib/libm.so when searching for -lm
ld: skipping incompatible /usr/bin/../lib/libm.a when searching for -lm
ld: skipping incompatible /usr/lib/libm.so when searching for -lm
ld: skipping incompatible /usr/lib/libm.a when searching for -lm
ld: cannot find -lm
./configure: line 854: ./testp: No such file or directory
Error: Unable to compile a C program using icc  -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE
    Please check your compiler settings or configure flags.
==========
A serial compilation error with GNU compilers on the same system
(using ./configure -static -noX11 gnu):
==========
$ arch
x86_64
$ cd amber11/AmberTools/src
$ make install 2> make.install.error
$ cat make.install.error
main.o: In function `create_file_names':
main.c:(.text+0x655): warning: the use of `mktemp' is dangerous, better use `mks
temp'
ar: creating arpack.a
ar: creating lapack.a
ar: creating blas.a
ar: creating lapack.a
ar: creating blas.a
ar: creating arpack.a
ar: creating lapack.a
ar: creating blas.a
ar: creating arpack.a
ar: creating libpdb.a
ar: creating arpack.a
ar: creating lapack.a
ar: creating blas.a
bind.c: In function 'rl_function_of_keyseq':
bind.c:704: warning: comparison is always true due to limited range of data type
display.c: In function 'rl_character_len':
display.c:1891: warning: comparison is always true due to limited range of data
type
fixbond.cpp:471: warning: unused parameter 'atms'
paren.cpp:14: warning: unused parameter 'mol'
solvate.cpp: In function 'void mort::solvate(mort::solute_i&, const mort::molecu
le_t&, const mort::region_i&)':
solvate.cpp:68: warning: unused variable 'svt_maxrad'
merge.cpp:103: warning: unused parameter 'prev'
ar: creating cifparse.a
/mnt/raidc/sally/ambertools.tabasco/amber11/bin/yacc: 3 shift/reduce conflicts.
./parse:  82 symbols.
./parse:  19 types, lastuser = 14, v_error = 14.
./parse:   9 classes.
./parse:   8 kinds.
./parse:   4 accesses.
./parse:  27 attributes.
./parse:  40 rules.
./parse:  40 used symbols.
./parse:  15 used types.
./parse:   7 used classes.
./parse:   7 used kinds.
./parse:   0 errors.
ar: creating libsff.a
ar: creating libpbsa.a
_safemem.f: In function 'reallocate_pointer_1d_character':
_safemem.f:914: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.
For Debian GNU/Linux specific bug reporting instructions,
see <URL:file:///usr/share/doc/gcc-4.1/README.Bugs>.
make[2]: *** [safemem.o] Error 1
make[1]: *** [librism] Error 2
make: *** [serial] Error 2
==========
A similar serial compilation error with GNU compilers on a different
system (using ./configure -static -noX11 gnu):
==========
$ arch
i686
$ cd amber11/AmberTools/src
$ make install 2> make.install.error
$ cat make.install.error
<snip>
ar: creating cifparse.a
/mnt/raidc/sally/testing_amber/31mar10_release_candidates/gnu/amber11/bin/yacc:
3 shift/reduce conflicts.
./parse:  82 symbols.
./parse:  19 types, lastuser = 14, v_error = 14.
./parse:   9 classes.
./parse:   8 kinds.
./parse:   4 accesses.
./parse:  27 attributes.
./parse:  40 rules.
./parse:  40 used symbols.
./parse:  15 used types.
./parse:   7 used classes.
./parse:   7 used kinds.
./parse:   0 errors.
ar: creating libsff.a
ar: creating libpbsa.a
_safemem.f: In function 'reallocate_pointer_1d_character':
_safemem.f:914: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.
For Debian GNU/Linux specific bug reporting instructions,
see <URL:file:///usr/share/doc/gcc-4.1/README.Bugs>.
make[2]: *** [safemem.o] Error 1
make[1]: *** [librism] Error 2
make: *** [serial] Error 2
==========
A parallel compilation error using Intel 11.1 compilers (using
./configure -static -noX11 -mpi intel):
==========
$ arch
i686
$ source /opt/intel/Compiler/11.1/056/bin/ifortvars.sh ia32
$ source /opt/intel/Compiler/11.1/056/bin/iccvars.sh ia32
$ source /opt/intel/Compiler/11.1/056/bin/ia32/idbvars.sh
$ source /opt/intel/Compiler/11.1/056/tbb/bin/tbbvars.sh ia32
$ source /opt/intel/Compiler/11.1/056/mkl/tools/environment/mklvars32.sh
$ export PATH=/opt/mpich2-1.0.7/bin:$PATH
$ which icc
/opt/intel/Compiler/11.1/056/bin/ia32/icc
$ which ifort
/opt/intel/Compiler/11.1/056/bin/ia32/ifort
$ which mpiexec
/opt/mpich2-1.0.7/bin/mpiexec
$ make parallel 2> make.parallel.error
$ cat make.parallel.error
<snip>
./parse:  82 symbols.
./parse:  19 types, lastuser = 14, v_error = 14.
./parse:   9 classes.
./parse:   8 kinds.
./parse:   4 accesses.
./parse:  27 attributes.
./parse:  40 rules.
./parse:  40 used symbols.
./parse:  15 used types.
./parse:   7 used classes.
./parse:   7 used kinds.
./parse:   0 errors.
nblist.c(883): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: totpair) \
          ^
eff.c(23): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: e_cons) private (i, rx, ry, rz, rw)
          ^
eff.c(99): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: e_bond) \
          ^
eff.c(199): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: e_theta) \
          ^
eff.c(366): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: e_tors) \
          ^
eff.c(992): warning #161: unrecognized #pragma
  #pragma omp parallel \
          ^
eff.c(1070): warning #161: unrecognized #pragma
  #pragma omp for schedule(dynamic, blocksize)
          ^
eff.c(1880): warning #161: unrecognized #pragma
  #pragma omp parallel \
          ^
eff.c(1921): warning #161: unrecognized #pragma
  #pragma omp for schedule(dynamic, blocksize)
          ^
gbsa.c(177): warning #267: the format string requires additional arguments
                    printf("egb: task %d received illegal value %d\n", i);
                                                                        ^
gbsa.c(271): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: totalvolume, surfacearea) \
          ^
gbsa.c(321): warning #161: unrecognized #pragma
  #pragma omp for schedule (dynamic, 1)
          ^
eff.c(2078): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: epol, elec, evdw, evdwnp) \
          ^
eff.c(2183): warning #161: unrecognized #pragma
  #pragma omp for schedule(dynamic, blocksize)
          ^
eff.c(2869): warning #161: unrecognized #pragma
  #pragma omp parallel \
          ^
eff.c(2929): warning #161: unrecognized #pragma
  #pragma omp for schedule(dynamic, blocksize)
          ^
egbr6.c(138): warning #161: unrecognized #pragma
  #pragma omp parallel \
          ^
egbr6.c(305): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: epol, elec, evdw) \
          ^
egbr6.c(613): warning #161: unrecognized #pragma
  #pragma omp parallel \
          ^
sff2.c(3452): warning #161: unrecognized #pragma
  #pragma omp parallel \
          ^
sff2.c(4339): warning #161: unrecognized #pragma
  #pragma omp parallel reduction (+: epol, elec, evdw, evdwnp) \
          ^
sff2.c(5681): warning #161: unrecognized #pragma
  #pragma omp barrier
          ^
sff2.c(7409): warning #161: unrecognized #pragma
  #pragma omp parallel private (i, j, i3, ii, jj, in9, threadnum, numthreads)
          ^
sff2.c(7589): warning #161: unrecognized #pragma
  #pragma omp parallel private (k, j, kk, jj, threadnum, numthreads)
          ^
sff2.c(7614): warning #161: unrecognized #pragma
  #pragma omp for
          ^
ar: creating libsff.a
make[2]: write error
make[1]: *** [libsff] Error 1
make[1]: write error
make: *** [parallel] Error 1
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Received on Sat Apr 10 2010 - 23:30:03 PDT