BAGEL编译求助

wxhwbh

不知道论坛上有没有用过这个程序的。问一个编译问题：按手册编译时有这么一步：

1. export BOOST_ROOT=/path/to/boost
   
2. $ export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH
   
3. 
   
4. $ ../configure --enable-mkl --with-boost=$BOOST_ROOT

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但是无论是系统自带的boost路径，还是自己下载的boost，配置时都会报这个错：

1. ...
   
2. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
   
3. checking how to hardcode library paths into programs... immediate
   
4. checking for boostlib >= 1.53... yes
   
5. checking whether the Boost::Regex library is available... yes
   
6. configure: error: Could not find a version of the Boost::Regex library!
   

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如果没有正确配置boost库，下一步make时会报错：

1. ...
   
2. /usr/include/boost/serialization/export.hpp:142:61:   required from ‘const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = bagel::SMITH::Tensor_<double>]’
   
3. ../../../src/smith/tensor.cc:167:1:   required from here
   
4. /usr/include/boost/serialization/access.hpp:118:9: 错误：‘class std::unordered_set<long unsigned int>’没有名为‘serialize’的成员
   

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所以想问问BAGEL要怎么正确编译呢？

zjxitcc

boost编译没通过的话，后面的步骤就不用看了。

“配置时都会报这个错”啥意思？配置谁？boost到底成功编译了没有？

beefly

ubuntu应用仓库已经有编译好的bagel了。装个ubuntu或衍生系统

hebrewsnabla

装了boost不等于装对了，你看看你有没有libboost_regex.so

如果有的话，看一下这个 https://github.com/qsimulate-open/bagel/issues/162
类似的问题有人问过了

wangxubo

我推测你就是单纯的没编译boost,boost不是一个单纯的头文件库,有的部分是需要编译的,照着官方手册编译一下boost

zjxitcc

wangxubo 发表于 2020-11-10 12:40
我推测你就是单纯的没编译boost,boost不是一个单纯的头文件库,有的部分是需要编译的,照着官方手册编译一下b ...

你的意思是他解压之后，啥也没做就开始写环境变量了么哈哈哈哈，有可能

我记得Eigen库就是这样的，解压即用。但是boost得编译。

wxhwbh

zjxitcc 发表于 2020-11-10 13:16
你的意思是他解压之后，啥也没做就开始写环境变量了么哈哈哈哈，有可能

我记得Eigen库就是这样的，解 ...

不是，在我的系统的/use/lib64里是有libboost_regex.so等库文件的。按四楼给的链接的做法，在./configure这一步里写成：

1. --with-boost=yes --with-boost-libdir=/usr/lib64

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那么./configure这一步就不会报错了。但下一步make还是会报错：

1. libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../../../src/smith -I../.. -I/usr/include -I../../.. -DNDEBUG -O3 -mavx -std=c++11 -MT tensor.lo -MD -MP -MF .deps/tensor.Tpo -c ../../../src/smith/tensor.cc  -fPIC -DPIC -o .libs/tensor.o
   
2. In file included from /usr/include/boost/serialization/split_member.hpp:23:0,
   
3.                  from /usr/include/boost/serialization/nvp.hpp:33,
   
4.                  from /usr/include/boost/serialization/array.hpp:19,
   
5.                  from ../../../btas/serialization.h:6,
   
6.                  from ../../../btas/varray/varray.h:6,
   
7.                  from ../../../btas/range.h:19,
   
8.                  from ../../../btas/defaults.h:15,
   
9.                  from ../../../btas/tensor.h:11,
   
10.                  from ../../../btas/generic/axpy_impl.h:8,
    
11.                  from ../../../btas/btas.h:8,
    
12.                  from ../../../src/util/math/btas_interface.h:38,
    
13.                  from ../../../src/util/math/vectorb.h:30,
    
14.                  from ../../../src/util/math/matrix_base.h:33,
    
15.                  from ../../../src/util/math/matrix.h:32,
    
16.                  from ../../../src/smith/tensor.h:34,
    
17.                  from ../../../src/smith/tensor.cc:28:
    
18. /usr/include/boost/serialization/access.hpp: In instantiation of ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’:
    
19. /usr/include/boost/serialization/serialization.hpp:69:69:   required from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’
    
20. /usr/include/boost/serialization/serialization.hpp:128:27:   required from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’
    
21. /usr/include/boost/archive/detail/iserializer.hpp:192:5:   required from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’
    
22. /usr/include/boost/archive/detail/iserializer.hpp:120:1:   required from ‘class boost::archive::detail::iserializer<boost::archive::binary_iarchive, std::unordered_set<long unsigned int> >’
    
23. /usr/include/boost/archive/detail/iserializer.hpp:387:13:   required from ‘static void boost::archive::detail::load_non_pointer_type<Archive>::load_standard::invoke(Archive&, const T&) [with T = std::unordered_set<long unsigned int>; Archive = boost::archive::binary_iarchive]’
    
24. /usr/include/boost/archive/detail/iserializer.hpp:439:28:   [ skipping 21 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
    
25. /usr/include/boost/serialization/export.hpp:86:1:   required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, bagel::SMITH::Tensor_<double> >’
    
26. /usr/include/boost/archive/detail/register_archive.hpp:25:8:   required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, bagel::SMITH::Tensor_<double> >’
    
27. /usr/include/boost/archive/binary_iarchive.hpp:96:1:   required by substitution of ‘template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = bagel::SMITH::Tensor_<double>]’
    
28. /usr/include/boost/serialization/export.hpp:132:58:   required from ‘void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = bagel::SMITH::Tensor_<double>; mpl_::false_ = mpl_::bool_<false>]’
    
29. /usr/include/boost/serialization/export.hpp:142:61:   required from ‘const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = bagel::SMITH::Tensor_<double>]’
    
30. ../../../src/smith/tensor.cc:167:1:   required from here
    
31. /usr/include/boost/serialization/access.hpp:118:9: 错误：‘class std::unordered_set<long unsigned int>’没有名为‘serialize’的成员
    
32.          t.serialize(ar, file_version);
    
33.          ^
    
34. /usr/include/boost/serialization/access.hpp: In instantiation of ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’:
    
35. /usr/include/boost/serialization/serialization.hpp:69:69:   required from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’
    
36. /usr/include/boost/serialization/serialization.hpp:128:27:   required from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’
    
37. /usr/include/boost/archive/detail/oserializer.hpp:152:5:   required from ‘void boost::archive::detail::oserializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’
    
38. /usr/include/boost/archive/detail/oserializer.hpp:101:1:   required from ‘class boost::archive::detail::oserializer<boost::archive::binary_oarchive, std::unordered_set<long unsigned int> >’
    
39. /usr/include/boost/archive/detail/oserializer.hpp:253:13:   required from ‘static void boost::archive::detail::save_non_pointer_type<Archive>::save_standard::invoke(Archive&, const T&) [with T = std::unordered_set<long unsigned int>; Archive = boost::archive::binary_oarchive]’
    
40. /usr/include/boost/archive/detail/oserializer.hpp:308:28:   [ skipping 21 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
    
41. /usr/include/boost/serialization/export.hpp:86:1:   required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_oarchive, bagel::SMITH::Tensor_<double> >’
    
42. /usr/include/boost/archive/detail/register_archive.hpp:25:8:   required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_oarchive, bagel::SMITH::Tensor_<double> >’
    
43. /usr/include/boost/archive/binary_oarchive.hpp:59:1:   required by substitution of ‘template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_oarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_oarchive*, boost::archive::detail::adl_tag) [with Serializable = bagel::SMITH::Tensor_<double>]’
    
44. /usr/include/boost/serialization/export.hpp:132:58:   required from ‘void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = bagel::SMITH::Tensor_<double>; mpl_::false_ = mpl_::bool_<false>]’
    
45. /usr/include/boost/serialization/export.hpp:142:61:   required from ‘const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = bagel::SMITH::Tensor_<double>]’
    
46. ../../../src/smith/tensor.cc:167:1:   required from here
    
47. /usr/include/boost/serialization/access.hpp:118:9: 错误：‘class std::unordered_set<long unsigned int>’没有名为‘serialize’的成员
    
48. make[3]: *** [tensor.lo] 错误 1
    
49. make[3]: 离开目录“/home/public/wbh/soft/bagel/obj/src/smith”
    
50. make[2]: *** [all-recursive] 错误 1
    
51. make[2]: 离开目录“/home/public/wbh/soft/bagel/obj/src”
    
52. make[1]: *** [all-recursive] 错误 1
    
53. make[1]: 离开目录“/home/public/wbh/soft/bagel/obj”
    
54. make: *** [all] 错误 2
    

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所以还是想问要怎么处理呢？

wxhwbh

hebrewsnabla 发表于 2020-11-9 23:12
装了boost不等于装对了，你看看你有没有libboost_regex.so

如果有的话，看一下这个 https://github.com/ ...

谢谢。libboost_regex.so在/usr/lib64里是有的。按照链接里的写法在./configure这一步里改成

1. --with-boost=yes --with-boost-libdir=/usr/lib64

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那么这一步就不会报错。
但是下一步make还是会报错：

1. libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../../../src/smith -I../.. -I/usr/include -I../../.. -DNDEBUG -O3 -mavx -std=c++11 -MT tensor.lo -MD -MP -MF .deps/tensor.Tpo -c ../../../src/smith/tensor.cc  -fPIC -DPIC -o .libs/tensor.o
   
2. In file included from /usr/include/boost/serialization/split_member.hpp:23:0,
   
3.                  from /usr/include/boost/serialization/nvp.hpp:33,
   
4.                  from /usr/include/boost/serialization/array.hpp:19,
   
5.                  from ../../../btas/serialization.h:6,
   
6.                  from ../../../btas/varray/varray.h:6,
   
7.                  from ../../../btas/range.h:19,
   
8.                  from ../../../btas/defaults.h:15,
   
9.                  from ../../../btas/tensor.h:11,
   
10.                  from ../../../btas/generic/axpy_impl.h:8,
    
11.                  from ../../../btas/btas.h:8,
    
12.                  from ../../../src/util/math/btas_interface.h:38,
    
13.                  from ../../../src/util/math/vectorb.h:30,
    
14.                  from ../../../src/util/math/matrix_base.h:33,
    
15.                  from ../../../src/util/math/matrix.h:32,
    
16.                  from ../../../src/smith/tensor.h:34,
    
17.                  from ../../../src/smith/tensor.cc:28:
    
18. /usr/include/boost/serialization/access.hpp: In instantiation of ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’:
    
19. /usr/include/boost/serialization/serialization.hpp:69:69:   required from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’
    
20. /usr/include/boost/serialization/serialization.hpp:128:27:   required from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’
    
21. /usr/include/boost/archive/detail/iserializer.hpp:192:5:   required from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::binary_iarchive; T = std::unordered_set<long unsigned int>]’
    
22. /usr/include/boost/archive/detail/iserializer.hpp:120:1:   required from ‘class boost::archive::detail::iserializer<boost::archive::binary_iarchive, std::unordered_set<long unsigned int> >’
    
23. /usr/include/boost/archive/detail/iserializer.hpp:387:13:   required from ‘static void boost::archive::detail::load_non_pointer_type<Archive>::load_standard::invoke(Archive&, const T&) [with T = std::unordered_set<long unsigned int>; Archive = boost::archive::binary_iarchive]’
    
24. /usr/include/boost/archive/detail/iserializer.hpp:439:28:   [ skipping 21 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
    
25. /usr/include/boost/serialization/export.hpp:86:1:   required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_iarchive, bagel::SMITH::Tensor_<double> >’
    
26. /usr/include/boost/archive/detail/register_archive.hpp:25:8:   required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, bagel::SMITH::Tensor_<double> >’
    
27. /usr/include/boost/archive/binary_iarchive.hpp:96:1:   required by substitution of ‘template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_iarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_iarchive*, boost::archive::detail::adl_tag) [with Serializable = bagel::SMITH::Tensor_<double>]’
    
28. /usr/include/boost/serialization/export.hpp:132:58:   required from ‘void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = bagel::SMITH::Tensor_<double>; mpl_::false_ = mpl_::bool_<false>]’
    
29. /usr/include/boost/serialization/export.hpp:142:61:   required from ‘const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = bagel::SMITH::Tensor_<double>]’
    
30. ../../../src/smith/tensor.cc:167:1:   required from here
    
31. /usr/include/boost/serialization/access.hpp:118:9: 错误：‘class std::unordered_set<long unsigned int>’没有名为‘serialize’的成员
    
32.          t.serialize(ar, file_version);
    
33.          ^
    
34. /usr/include/boost/serialization/access.hpp: In instantiation of ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’:
    
35. /usr/include/boost/serialization/serialization.hpp:69:69:   required from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’
    
36. /usr/include/boost/serialization/serialization.hpp:128:27:   required from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’
    
37. /usr/include/boost/archive/detail/oserializer.hpp:152:5:   required from ‘void boost::archive::detail::oserializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::binary_oarchive; T = std::unordered_set<long unsigned int>]’
    
38. /usr/include/boost/archive/detail/oserializer.hpp:101:1:   required from ‘class boost::archive::detail::oserializer<boost::archive::binary_oarchive, std::unordered_set<long unsigned int> >’
    
39. /usr/include/boost/archive/detail/oserializer.hpp:253:13:   required from ‘static void boost::archive::detail::save_non_pointer_type<Archive>::save_standard::invoke(Archive&, const T&) [with T = std::unordered_set<long unsigned int>; Archive = boost::archive::binary_oarchive]’
    
40. /usr/include/boost/archive/detail/oserializer.hpp:308:28:   [ skipping 21 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
    
41. /usr/include/boost/serialization/export.hpp:86:1:   required from ‘struct boost::archive::detail::ptr_serialization_support<boost::archive::binary_oarchive, bagel::SMITH::Tensor_<double> >’
    
42. /usr/include/boost/archive/detail/register_archive.hpp:25:8:   required from ‘struct boost::archive::detail::_ptr_serialization_support<boost::archive::binary_oarchive, bagel::SMITH::Tensor_<double> >’
    
43. /usr/include/boost/archive/binary_oarchive.hpp:59:1:   required by substitution of ‘template<class Serializable> typename boost::archive::detail::_ptr_serialization_support<boost::archive::binary_oarchive, Serializable>::type boost::archive::detail::instantiate_ptr_serialization(Serializable*, boost::archive::binary_oarchive*, boost::archive::detail::adl_tag) [with Serializable = bagel::SMITH::Tensor_<double>]’
    
44. /usr/include/boost/serialization/export.hpp:132:58:   required from ‘void boost::archive::detail::extra_detail::guid_initializer<T>::export_guid(mpl_::false_) const [with T = bagel::SMITH::Tensor_<double>; mpl_::false_ = mpl_::bool_<false>]’
    
45. /usr/include/boost/serialization/export.hpp:142:61:   required from ‘const boost::archive::detail::extra_detail::guid_initializer<T>& boost::archive::detail::extra_detail::guid_initializer<T>::export_guid() const [with T = bagel::SMITH::Tensor_<double>]’
    
46. ../../../src/smith/tensor.cc:167:1:   required from here
    
47. /usr/include/boost/serialization/access.hpp:118:9: 错误：‘class std::unordered_set<long unsigned int>’没有名为‘serialize’的成员
    
48. make[3]: *** [tensor.lo] 错误 1
    
49. make[3]: 离开目录“/home/public/wbh/soft/bagel/obj/src/smith”
    
50. make[2]: *** [all-recursive] 错误 1
    
51. make[2]: 离开目录“/home/public/wbh/soft/bagel/obj/src”
    
52. make[1]: *** [all-recursive] 错误 1
    
53. make[1]: 离开目录“/home/public/wbh/soft/bagel/obj”
    
54. make: *** [all] 错误 2
    

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wangxubo

wxhwbh 发表于 2020-11-10 14:30
不是，在我的系统的/use/lib64里是有libboost_regex.so等库文件的。按四楼给的链接的做法，在./configure ...

不要用源里的boost,自己编译一遍boost,确保boost用的编译器和编译bagel用的编译器一样.

hebrewsnabla

wxhwbh 发表于 2020-11-10 14:33
谢谢。libboost_regex.so在/usr/lib64里是有的。按照链接里的写法在./configure这一步里改成

那么这一 ...

我make并无问题。

不过我的gcc和boost都是最新的，没有兼容问题。估计你的不是，你可能得按照9楼的建议自己编译boost。

wxhwbh

找到解决方法了，在编译boost后进入boost的头文件目录的propetry_tree目录（我的是/usr/local/include/boost/propetry_tree），编辑ptree_serialization.hpp, 找到下面这个namespace（前面数字是行号）：
...
51      namespace detail
52     {      
53         template <class Archive, class K, class D, class C>
54         inline void load_children(Archive &ar,
55                                   basic_ptree<K, D, C> &t)
56         {   
57             namespace bsl = boost::serialization;
58             namespace bsa = boost::archive;
59            
60             typedef basic_ptree<K, D, C> tree;
61             typedef typename tree::value_type value_type;
62            
63             bsl::collection_size_type count;
64             ar >> BOOST_SERIALIZATION_NVP(count);
65             bsl::item_version_type item_version(0);
66             const bsa::library_version_type library_version(
67                 ar.get_library_version()
68             );
69             if(bsa::library_version_type(3) < library_version){
...

把标记的bsa改成bsl，然后重新编译就没问题了。

biogon

beefly 发表于 2020-11-9 22:28
ubuntu应用仓库已经有编译好的bagel了。装个ubuntu或衍生系统

还是最新版本的，一键安装就能用，并行啥的都有了

abin

测试全通过，
intel2020 update2 全套。
BAGEL v1.2.2。

Accelerator

我按照http://bbs.keinsci.com/thread-27002-1-1.html的方法编译BAGEL时也出现了类似的现象，不过与楼主不同的是写--with-boost=yes --with-boost-libdir=/usr/local/lib/后就可以解决，并且后续make时一切正常。无论是自己编译的boost 1.71.0还是ubuntu apt安装的boost都可以。另外如果按照11楼的做法修改命名空间，反而会造成make时报错。
用apt-get安装BAGEL虽然方便，并且也可以并行（需要apt安装openblas，否则只能单核运算；不要使用mpirun，装了openblas后直接BAGEL xxx.json，就可以自动并行），但并行效率很低，CPU占用率在100%到满核之间反复横跳。还是要自己编译。
用mpirun BAGEL运行时记得修改MKL_NUM_THREADS和BAGEL_NUM_THREADS两个环境变量，我测试的结果是设为1到2效率比较高。如果按照默认值，则并行时反而比串行要慢10倍左右。

喵星大佬

Accelerator 发表于 2022-1-5 14:29
我按照http://bbs.keinsci.com/thread-27002-1-1.html的方法编译BAGEL时也出现了类似的现象，不过与楼主不 ...

确实，是1-2核每个mpi比较快，但不是所有功能都可以mpi并行