Problems about compilation

[magician-david]

Hello! I met a problem when I typed the command:

cmake .. -DEIGEN3_INCLUDE_DIR=eigen -DCMAKE_CXX_COMPILER=/usr/bin/clang++

The message was:

~/LSTM-ER/build$ cmake .. -DEIGEN3_INCLUDE_DIR=../eigen -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -- Boost version: 1.57.0 -- Found the following Boost libraries: -- program_options -- serialization CMake Error at CMakeLists.txt:23 (find_package): By not providing "FindEigen3.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "Eigen3", but CMake did not find one.

Could not find a package configuration file provided by "Eigen3" with any of the following names:

Eigen3Config.cmake
eigen3-config.cmake

Add the installation prefix of "Eigen3" to CMAKE_PREFIX_PATH or set "Eigen3_DIR" to a directory containing one of the above files. If "Eigen3" provides a separate development package or SDK, be sure it has been installed.

-- Configuring incomplete, errors occurred! See also "~/LSTM-ER/build/CMakeFiles/CMakeOutput.log". See also "~/LSTM-ER/build/CMakeFiles/CMakeError.log".

I guess you have lost a command:

tar xzf cnn.tar.gz tar xzf eigen.tar.gz cd eigen mkdir build cd build cmake .. -DEIGEN3_INCLUDE_DIR=eigen -DCMAKE_CXX_COMPILER=/usr/bin/clang++ make cd ..

[Diego999]

I got the same problem as you, but compiling within the eigen directory doesn't create all the needed stuff like the build/relation/RelationExtraction. Are you sure about it ?

[magician-david]

Sorry, it can't fix all of the problem. But we do need to build and install Eigen first. Then we can follow the instructions. Maybe these would be helpful:

tar xzf cnn.tar.gz tar xzf eigen.tar.gz cd eigen mkdir build cd build cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/clang++ make install cd ../.. mkdir build cd build cmake .. -DEIGEN3_INCLUDE_DIR=eigen -DCMAKE_CXX_COMPILER=/usr/bin/clang++ make cd ..

I have fixed the compiling problem. But I don't remember all the details. By the way, I have met another problem when I test the model. I think we can discuss it.

[Diego999]

Thanks for you answer, I still had to fix some CMakeLists files but I could compile. However, I have a similar problem as you, for both training and testing, I have exactly "Segmentation fault". Do you have the same ?

$ build/relation/RelationExtraction --train -y yaml/parameter-semeval-2010.yaml 306560 words, 200 dimensions start loading documents in data/semeval-2010/corpus/train/ Segmentation fault

$ build/relation/RelationExtraction --test -y yaml/parameter-semeval-2010.yaml 306560 words, 200 dimensions Segmentation fault

I have investigated and have found that function is_directory(p) always returns false even if the path is really a directory, and so the training set is not loaded.

[magician-david]

Have you preprocessed the data according to the data/README.md? I think it will fix the training problem on SemEval dataset.

[Diego999]

Yes I did it and have exactly the files .txt, .txt.conll, .ann, .stanford.so. By the way it works on my virtual machine on Fedora.

[Diego999]

What was your problem during the testing ? Something like

unknown label:B-Term, treated as negative unknown label:L-Term, treated as negative unknown label:U-Term, treated as negative

For all samples in the testing set ?

EDIT : After re-training the model, it works on the testing set. However, the direction are always e1 -> e2 (except for the negative classes)

[magician-david]

Yes! I got the same problem! In some cases the .pred.ann files are empty.

It seems that we can't test during the training process?

How to get the Macro F1-score when testing the model?

[Diego999]

I guess that empty .pred.ann files mean that the sample is the class Other (negative class).

I did the whole training this morning, and got similar results : testing always 0/0/0. Afterwards, I used the trained model on the testing set (because it didn't work with the already retrained model) and obtained the relations without direction. An example of output is Product-Producer Arg1:T0 Arg2:T0 for the sample 8023, but the relation direction is not specified (T0->T0 rather than T1->T2 or T2->T1).

In term of relation classification, without direction, I used the predictions directly in the official scorer of SemEval-2010 Task 8 and got a macro average F1 (excluding others) around 0.86-0.88 (don't remember exactly).

I don't know what we should do in order to have also the direction (and so, having a non nul P/R/F on the testing during the training and afterwards)

[magician-david]

I tried "build/relation/RelationExtraction --test -y yaml/parameter-semeval-2010.yaml" several days before and I got the same result. But I haven't used the official scorer yet. Thanks.

[Diego999]

Don't forger that the official scorer give you two things :

• (9+1)-WAY EVALUATION IGNORING DIRECTIONALITY, where you should obtain ~0.86-0.88
• (9+1)-WAY EVALUATION TAKING DIRECTIONALITY INTO ACCOUNT -- OFFICIAL, where you cannot use due to the direction missing from the *.pred.ann

I'll check why it outputs always T0->T0 for each relation rather than using T1, T2. If you find why, I would be interested !

[Diego999]

I solved the problem. If you want to have the direction and have the correct format to feed directly the official scorer, you should modify RelLstmModel.cpp:568

if(dict_.is_reverse_relation(besti)){
                int rbesti = dict_.reverse_relation(besti); // normalize
                string rel_type = dict_.get_rel_string(rbesti);
                vector<string> rels;
                split(rels, rel_type, bind2nd(equal_to<char>(), ':'));
                ofs << rels[1] << " ";
                ofs << "Arg1:T" << ent_map[cell->row()] << " ";
                ofs << "Arg2:T" << ent_map[cell->col()] << endl;
              }else{
                string rel_type = dict_.get_rel_string(besti);
                vector<string> rels;
                split(rels, rel_type, bind2nd(equal_to<char>(), ':'));
                ofs << rels[1] << " ";
                ofs << "Arg1:T" << ent_map[cell->col()] << " ";
                ofs << "Arg2:T" << ent_map[cell->row()] << endl;
              }

to

 if(dict_.is_reverse_relation(besti)){
                int rbesti = dict_.reverse_relation(besti); // normalize
                string rel_type = dict_.get_rel_string(rbesti);
                vector<string> rels;
                split(rels, rel_type, bind2nd(equal_to<char>(), ':'));
                ofs << rels[1] << "(e2,e1)";
              }else{
                string rel_type = dict_.get_rel_string(besti);
                vector<string> rels;
                split(rels, rel_type, bind2nd(equal_to<char>(), ':'));
                ofs << rels[1] << "(e1,e2)";
              }

With this, I obtain a score of 84.87, which is similar to the results of the paper, without the use of external resources

[magician-david]

Perfect! And my score is 83.73. :)

[mmiwa]

I fixed the reported compilation problem by updating cnn.tar.gz, so I close this.

[hi-wangyan]

@magician-david hello, I meet a mistake like follow,can you give me some help?Thank you!

cmake .. -DEIGEN3_INCLUDE_DIR=eigen -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -- The CXX compiler identification is unknown CMake Error at CMakeLists.txt:1 (project): The CMAKE_CXX_COMPILER:

/usr/bin/clang++

is not a full path to an existing compiler tool.

Tell CMake where to find the compiler by setting either the environment variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH.

-- Configuring incomplete, errors occurred! See also "/home/wangyan/PycharmProjects/LSTM-ER-master/build/CMakeFiles/CMakeOutput.log". See also "/home/wangyan/PycharmProjects/LSTM-ER-master/build/CMakeFiles/CMakeError.log".