[SCIP] pyscipopt installation query

Kamp, Dominik Dominik.Kamp at uni-bayreuth.de
Wed Jul 12 10:24:34 CEST 2023 

Dear Welma,

thank you for the details.

> Am 27.06.2023 um 04:58 schrieb Welma <mogitiwelma at gmail.com>:
> 
> Dear Jonas,
> 
> Here is some additional information but I am not sure if this influences the installation of pyscipopt.
> I am doing the installation in linux ubuntu. 
> When installing the SCIP suite after the build configuration stage, I proceeded with the SCIP compilation process. It is in this stage that I noted the following warning:
> 
> [ 7%] Building Fortran object papilo/CMakeFiles/clusol.dir/src/papilo/external/lusol/src/lusol_precision.f90.o
> f951: Warning: Nonexistent include directory ‘/home/welma/Documents/scipoptsuite-8.0.3/papilo/external’ [-Wmissing-include-dirs]
> [ 7%] Building Fortran object papilo/CMakeFiles/clusol.dir/src/papilo/external/lusol/src/lusol.f90.o
> f951: Warning: Nonexistent include directory ‘/home/welma/Documents/scipoptsuite-8.0.3/papilo/external’ [-Wmissing-include-dirs]
> [ 8%] Building Fortran object papilo/CMakeFiles/clusol.dir/src/papilo/external/lusol/src/lusol6b.f.o
> f951: Warning: Nonexistent include directory ‘/home/welma/Documents/scipoptsuite-8.0.3/papilo/external’ [-Wmissing-include-dirs]
> [ 8%] Building Fortran object papilo/CMakeFiles/clusol.dir/src/papilo/external/lusol/src/lusol7b.f.o
> f951: Warning: Nonexistent include directory ‘/home/welma/Documents/scipoptsuite-8.0.3/papilo/external’ [-Wmissing-include-dirs]
> [ 8%] Building Fortran object papilo/CMakeFiles/clusol.dir/src/papilo/external/lusol/src/lusol8b.f.o
> f951: Warning: Nonexistent include directory ‘/home/welma/Documents/scipoptsuite-8.0.3/papilo/external’ [-Wmissing-include-dirs]
> [ 8%] Building Fortran object papilo/CMakeFiles/clusol.dir/src/papilo/external/lusol/src/lusol_util.f.o
> f951: Warning: Nonexistent include directory ‘/home/welma/Documents/scipoptsuite-8.0.3/papilo/external’ [-Wmissing-include-dirs]

These warnings will be resolved in the next bugfix release.

> It was then followed by this after a few seconds. I appears severally whenever this appears "Building CXX object scip/src/CMakeFiles/libscip.dir/scip/presol_milp.cpp.o"
> 
> 
> In file included from /usr/include/string.h:535,
> from /usr/include/c++/11/cstring:42,
> from /usr/include/boost/container_hash/detail/hash_float.hpp:21,
> from /usr/include/boost/container_hash/hash.hpp:22,
> from /usr/include/boost/functional/hash.hpp:6,
> from /usr/include/boost/multiprecision/float128.hpp:11,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/misc/MultiPrecision.hpp:34,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/core/SparseStorage.hpp:27,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/core/MatrixBuffer.hpp:27,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/test/papilo/core/MatrixBufferTest.cpp:24:
> In function ‘void* memmove(void*, const void*, size_t)’,
> inlined from ‘F boost::container::dtl::memmove(I, I, F) [with I = int*; F = int*]’ at /usr/include/boost/container/detail/copy_move_algo.hpp:182:19,
> inlined from ‘typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = boost::container::small_vector_allocator<int, std::allocator<void>, void>; I = int*; F = int*]’ at /usr/include/boost/container/detail/copy_move_algo.hpp:320:23,
> inlined from ‘void boost::container::vector<T, Allocator, Options>::priv_forward_range_insert_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_move_proxy<boost::container::small_vector_allocator<int, std::allocator<void>, void>, int*>; T = int; A = boost::container::small_vector_allocator<int, std::allocator<void>, void>; Options = void]’ at /usr/include/boost/container/vector.hpp:2999:13,
> inlined from ‘boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_forward_range_insert_no_capacity(const pointer&, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy, boost::container::version_1) [with InsertionProxy = boost::container::dtl::insert_move_proxy<boost::container::small_vector_allocator<int, std::allocator<void>, void>, int*>; T = int; A = boost::container::small_vector_allocator<int, std::allocator<void>, void>; Options = void]’ at /usr/include/boost/container/vector.hpp:2732:10,
> inlined from ‘void boost::container::vector<T, Allocator, Options>::priv_push_back(U&&) [with U = int; T = int; A = boost::container::small_vector_allocator<int, std::allocator<void>, void>; Options = void]’ at /usr/include/boost/container/vector.hpp:2625:10,
> inlined from ‘void boost::container::vector<T, Allocator, Options>::push_back(T&&) [with T = int; A = boost::container::small_vector_allocator<int, std::allocator<void>, void>; Options = void]’ at /usr/include/boost/container/vector.hpp:1876:4,
> inlined from ‘const papilo::MatrixEntry<REAL>* papilo::MatrixBuffer<REAL>::begin(papilo::SmallVec<int, 32>&) const [with bool RowMajor = false; REAL = double]’ at /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/core/MatrixBuffer.hpp:296:22,
> inlined from ‘void ____C_A_T_C_H____T_E_S_T____0()’ at /home/welma/Documents/scipoptsuite-8.0.3/papilo/test/papilo/core/MatrixBufferTest.cpp:155:23:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:36:34: warning: ‘void* __builtin_memmove(void*, const void*, long unsigned int)’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=]
> 
> 36 | return __builtin___memmove_chk (__dest, __src, __len,
> | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
> 37 | __glibc_objsize0 (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from /usr/include/x86_64-linux-gnu/c++/11/bits/c++allocator.h:33,
> from /usr/include/c++/11/bits/allocator.h:46,
> from /usr/include/c++/11/memory:64,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/misc/MultiPrecision.hpp:30,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/core/SparseStorage.hpp:27,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/src/papilo/core/MatrixBuffer.hpp:27,
> from /home/welma/Documents/scipoptsuite-8.0.3/papilo/test/papilo/core/MatrixBufferTest.cpp:24:
> /usr/include/c++/11/ext/new_allocator.h: In function ‘void ____C_A_T_C_H____T_E_S_T____0()’:
> /usr/include/c++/11/ext/new_allocator.h:127:48: note: at offset 4 into destination object of size 4 allocated by ‘operator new’
> 127 | return static_cast<_Tp*>(::operator new(__n * sizeof(_Tp)));
> | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
> /usr/include/c++/11/ext/new_allocator.h:127:48: note: at offset [5, 8] into destination object of size 4 allocated by ‘operator new’

These warnings should be resolved with GCC >= 12.3.

> Is this something I need to sort out first before proceeding to the pyscipopt installation?

No, the warnings should not disturb the pyscipopt-Installation.

It might be that the variable SCIPOPTDIR is still not set correctly. As described in https://github.com/scipopt/PySCIPOpt/blob/master/INSTALL.md it should be set to the installation path containing lib and include. If you have installed scip using 'make install', the installation path depends on your system (for me it is '/usr/local'). You can also specify the installation path by adding the cmake argument -DCMAKE_INSTALL_PREFIX=<path> while replacing <path> with the desired location.

> Many thanks.

Best regards,

Dominik

> On Tue, Jun 27, 2023 at 9:42 AM Welma <mogitiwelma at gmail.com> wrote:
> Dear Jonas,
> 
> My bad that was a typo error but even with the correction it still gives the same error.
> 
> Thanks.
> 
> On Mon, Jun 26, 2023 at 9:10 PM Jonas Charfreitag <jcharfreitag at uni-bonn.de> wrote:
> Dear Welma,
> just to rule out a simple explanation:
> At least in the copy of the terminal output in your mail, the SCIPOPTDIR path seems off.
>> SCIPOPTDIR=/Documents/scipoptsuite-8.o.3/ does not contain an include directory; searching for include files in src or ../src directory.
> The the zero of the scipoptsuite is an o. Is this really the correct path?
> 
> Best
> Jonas
> 
> On 6/26/23 08:57, Welma wrote:
>> Hello SCIP experts,
>> 
>> Currently trying to install PySCIPOpt but I am getting the error below. My SCIP installation is working. 
>> 
>> 
>> welma at welma-HP-EliteBook:~$ python3 -m pip install pyscipopt
>> Defaulting to user installation because normal site-packages is not writeable
>> Collecting pyscipopt
>>   Using cached PySCIPOpt-4.3.0.tar.gz (665 kB)
>>   Installing build dependencies ... done
>>   Getting requirements to build wheel ... error
>>   error: subprocess-exited-with-error
>>   
>>   × Getting requirements to build wheel did not run successfully.
>>   │ exit code: 1
>>   ╰─> [2 lines of output]
>>       SCIPOPTDIR=/Documents/scipoptsuite-8.o.3/ does not contain an include directory; searching for include files in src or ../src directory.
>>       Could not find a src directory in SCIPOPTDIR=/Documents/scipoptsuite-8.o.3/; maybe it points to a wrong directory.
>>       [end of output]
>>   
>>   note: This error originates from a subprocess, and is likely not a problem with pip.
>> error: subprocess-exited-with-error
>> 
>> × Getting requirements to build wheel did not run successfully.
>> │ exit code: 1
>> ╰─> See above for output.
>> 
>> note: This error originates from a subprocess, and is likely not a problem with pip.
>>  
>> Note: In the build process, only the lib subdirectory was created in the build directory. 
>> Is the include subdirectory also supposed to be created in the build folder? On searching the header files meant to be in the 'include' subdirectory, they are there but in different folders. Kindly advice on how to solve this error
>> 
>> Many thanks.
>> 
>> -- 
>> Regards,
>> Welma Nyabuto
>> Researcher......phd student
>> Gifu University
>> 
>> 
>> _______________________________________________
>> Scip mailing list
>> Scip at zib.de
>> https://listserv.zib.de/mailman/listinfo/scip
>> 
> -- 
> M.Sc. Jonas Charfreitag
> Uni Bonn - Institut fuer Informatik - Abteilung 1
> Friedrich-Hirzebruch-Allee 8 / Room 2.078a
> 53115 Bonn, Germany
> 
> e-mail: jcharfreitag at uni-bonn.de
> web: https://ca.cs.uni-bonn.de/doku.php?id=people:charfreitag
> 
> 
> 
> -- 
> Regards,
> Welma Nyabuto
> Researcher......phd student
> Gifu University
> 
> 
> 
> -- 
> Regards,
> Welma Nyabuto
> Researcher......phd student
> Gifu University
> 
> _______________________________________________
> Scip mailing list
> Scip at zib.de
> https://listserv.zib.de/mailman/listinfo/scip

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