openmopac/mopac

Compilation problem with latest github pull (27.06.2022)

Closed this issue · 6 comments

flatstik commented 

  246 |           text = koment(1:i)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 240 bytes from a region of size 120
[-Wstringop-overflow=]
/tmp/mopac/src/output/writmo.F90:952:0:

  952 |           line = archive_fn(:len_trim(archive_fn) - 3)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/tmp/mopac/src/output/writmo.F90:953:0:

  953 |           line = archive_fn(:len_trim(archive_fn) - 3)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/tmp/mopac/src/reactions/big_swap.F90:1491:0:

 1491 |     line = input_fn(:len_trim(input_fn) - 5)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/tmp/mopac/src/reactions/big_swap.F90:1523:0:

 1523 |       line = input_fn(:len_trim(input_fn) - 5)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/tmp/mopac/src/reactions/big_swap.F90:628:0:

  628 |     line = input_fn(:len_trim(input_fn) - 5)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/tmp/mopac/src/reactions/big_swap.F90:649:0:

  649 |     line = input_fn(:len_trim(input_fn) - 5)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/tmp/mopac/src/reactions/big_swap.F90:697:0:

  697 |     line = input_fn(:len_trim(input_fn) - 5)
      | 
Warning: '?'�'?'__builtin_memcpy'?'�'?' reading 3000 bytes from a region of size 241
[-Wstringop-overflow=]
/usr/bin/ld: libmopac.so.1: undefined reference to `omp_get_max_threads_'
/usr/bin/ld: libmopac.so.1: undefined reference to `omp_set_num_threads_'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/mopac-param.dir/build.make:89: mopac-param] Error 1
make[1]: *** [CMakeFiles/Makefile2:699: CMakeFiles/mopac-param.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

COLLECT_GCC=gfortran-9
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu
9.4.0-1ubuntu1~20.04.1' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs
--enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr
--with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu-
--enable-shared --enable-linker-build-id --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls
--enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes
--with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify
--enable-plugin --enable-default-pie --with-system-zlib
--with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch
--disable-werror --with-arch-32=i686 --with-abi=m64
--with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic
--enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa
--without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.1)

Sorry for the UTF-problem (�-marks), that's because of copypasteing the error message to my e-mail system.

susilehtola commented

Please check that your repository is up to date; this is issue #76 that was fixed by #77...

susilehtola commented

Configured with: ../src/configure -v --with-pkgversion='Ubuntu

MOPAC does not have configure so I wonder where this is from...

flatstik commented

Please check that your repository is up to date; this is issue #76 that was fixed by #77...

I'm confident - pulled it yesterday and tried to compile. No problems with cmake ., but make gave those problems.

Configured with: ../src/configure -v --with-pkgversion='Ubuntu

MOPAC does not have configure so I wonder where this is from...

That's the output from gcc -v (indicating gfortran version as well)

flatstik commented

With my personal computer, I have following problem (this is with pull 27.06.2022 few minutes before posting this):

/tmp/mopac/src/chemistry/add_hydrogen_atoms.F90:190:0:

        line = line(i + 1: j - 1)
 
Warning: ‘__builtin_memmove’ reading 3000 bytes from a region of size 2999 [-Wstringop-overflow=]

/usr/bin/ld: libmopac.so.1: undefined reference to `omp_get_max_threads_'
/usr/bin/ld: libmopac.so.1: undefined reference to `omp_set_num_threads_'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/mopac.dir/build.make:89: mopac] Error 1
make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/mopac.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

gfortran -v gives following:

Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/8/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 8.3.0-6' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 8.3.0 (Debian 8.3.0-6)

Almost same error with my personal computational server:

[ 99%] Built target mopac-core
Scanning dependencies of target mopac-param
[ 99%] Building Fortran object CMakeFiles/mopac-param.dir/src/param.F90.o
[100%] Linking Fortran executable mopac-param
/usr/bin/ld: libmopac.so.1: undefined reference to `omp_get_max_threads_'
/usr/bin/ld: libmopac.so.1: undefined reference to `omp_set_num_threads_'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/mopac-param.dir/build.make:112: mopac-param] Error 1
make[1]: *** [CMakeFiles/Makefile2:709: CMakeFiles/mopac-param.dir/all] Error 2
make: *** [Makefile:182: all] Error 2

Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-Km9U7s/gcc-10-10.2.1/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 10.2.1 20210110 (Debian 10.2.1-6)
susilehtola commented

Hm, I can actually reproduce this. @godotalgorithm's changes to #77 broke the commit

godotalgorithm commented

This should be fixed now. I overlooked compile-time vs. link-time flags in tweaking Susi's original fix to this problem, and I directly verified that the problem remains fixed by my tweaks this time around.