compile error

[tianshilu]

Hi @schristley @acrinklaw ,

I git clone the repository and tried to compile it. cmake . runs successfully. But there is an error message when I execute cmake --build . (shown below)

My cmake version is 3.20.4. Could you give me a hint on how to fix the problem?

Thanks!

[acrinklaw]

Hi @tianshilu, what version of gcc do you have? This is most likely an issue of having a different version of gcc (which implements openmp) than is required.

[tianshilu]

Hi @acrinklaw Thanks for your prompt response. I attached my gcc version.

[acrinklaw]

No problem at all. I would suggest trying to update your gcc to the highest you can on ubuntu 18.04, when I wrote this I was using gcc 9.X. If it still gives you issues I will troubleshoot. I will also add some logic to CMake to make sure that everything is compatible for future users. Thanks!

[tianshilu]

Thank you for your suggestion. I will upgrade gcc. Will keep you posted. Appreciate your help!

[tianshilu]

I have one additional question. I tried to download the package https://github.com/IEDB/TCRMatch/releases/download/v0.1.0/TCRMatch_v0.1.0_Linux.tar.gzhttps://github.com/IEDB/TCRMatch/releases/download/v0.1.0/TCRMatch_v0.1.0_Linux.tar.gz which is already complied. I could not execute it and the error message is ‘segmentation fault (core dump)’. Do you know what the problem is?

On Jun 16, 2021, at 11:59 PM, Austin Crinklaw @.***> wrote:

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No problem at all. I would suggest trying to update your gcc to the highest you can on ubuntu 18.04, when I wrote this I was using gcc 9.X. If it still gives you issues I will troubleshoot. I will also add some logic to CMake to make sure that everything is compatible for future users. Thanks!

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[acrinklaw]

Yeah I believe that is because I compiled that binary in a different environment than you have. It was a mistake on my part - I'm still learning C++ development practices :-) It is getting late here but tomorrow I will see how people go about properly sharing binaries. For now I still suggest trying to upgrade gcc and compiling TCRMatch

[tianshilu]

I upgraded gcc to 9.4.0 and compiled TCRMatch. It seems the same error "invalid controlling predicate" existed. Do you have other suggestions to fix the problem?

[acrinklaw]

Hmm that is quite strange. The error is suggesting something is wrong with the parallelized for loops that are using openMP. I am unable to recreate it locally. Would you mind attaching the code from tcrmatch.cpp? In addition can you attach the output from echo |cpp -fopenmp -dM |grep -i open? Thank you

[tianshilu]

The output is: #define _OPENMP 201511 It doesn't allow me attach the *cpp file here. So I pasted the code here. Let me know if it is not convenient for you. I can send you an email. Thanks for your help!

include

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include

include

std::array<std::array<float, 20>, 20> k1; int p_kmin = 1; int p_kmax = 30; float p_beta = 0.11387; // Hardcoded because parsing + computing matrix is annoying float blm_qij[20][20] = { {0.0215, 0.0023, 0.0019, 0.0022, 0.0016, 0.0019, 0.003, 0.0058, 0.0011, 0.0032, 0.0044, 0.0033, 0.0013, 0.0016, 0.0022, 0.0063, 0.0037, 0.0004, 0.0013, 0.0051}, {0.0023, 0.0178, 0.002, 0.0016, 0.0004, 0.0025, 0.0027, 0.0017, 0.0012, 0.0012, 0.0024, 0.0062, 0.0008, 0.0009, 0.001, 0.0023, 0.0018, 0.0003, 0.0009, 0.0016}, {0.0019, 0.002, 0.0141, 0.0037, 0.0004, 0.0015, 0.0022, 0.0029, 0.0014, 0.001, 0.0014, 0.0024, 0.0005, 0.0008, 0.0009, 0.0031, 0.0022, 0.0002, 0.0007, 0.0012}, {0.0022, 0.0016, 0.0037, 0.0213, 0.0004, 0.0016, 0.0049, 0.0025, 0.001, 0.0012, 0.0015, 0.0024, 0.0005, 0.0008, 0.0012, 0.0028, 0.0019, 0.0002, 0.0006, 0.0013}, {0.0016, 0.0004, 0.0004, 0.0004, 0.0119, 0.0003, 0.0004, 0.0008, 0.0002, 0.0011, 0.0016, 0.0005, 0.0004, 0.0005, 0.0004, 0.001, 0.0009, 0.0001, 0.0003, 0.0014}, {0.0019, 0.0025, 0.0015, 0.0016, 0.0003, 0.0073, 0.0035, 0.0014, 0.001, 0.0009, 0.0016, 0.0031, 0.0007, 0.0005, 0.0008, 0.0019, 0.0014, 0.0002, 0.0007, 0.0012}, {0.003, 0.0027, 0.0022, 0.0049, 0.0004, 0.0035, 0.0161, 0.0019, 0.0014, 0.0012, 0.002, 0.0041, 0.0007, 0.0009, 0.0014, 0.003, 0.002, 0.0003, 0.0009, 0.0017}, {0.0058, 0.0017, 0.0029, 0.0025, 0.0008, 0.0014, 0.0019, 0.0378, 0.001, 0.0014, 0.0021, 0.0025, 0.0007, 0.0012, 0.0014, 0.0038, 0.0022, 0.0004, 0.0008, 0.0018}, {0.0011, 0.0012, 0.0014, 0.001, 0.0002, 0.001, 0.0014, 0.001, 0.0093, 0.0006, 0.001, 0.0012, 0.0004, 0.0008, 0.0005, 0.0011, 0.0007, 0.0002, 0.0015, 0.0006}, {0.0032, 0.0012, 0.001, 0.0012, 0.0011, 0.0009, 0.0012, 0.0014, 0.0006, 0.0184, 0.0114, 0.0016, 0.0025, 0.003, 0.001, 0.0017, 0.0027, 0.0004, 0.0014, 0.012}, {0.0044, 0.0024, 0.0014, 0.0015, 0.0016, 0.0016, 0.002, 0.0021, 0.001, 0.0114, 0.0371, 0.0025, 0.0049, 0.0054, 0.0014, 0.0024, 0.0033, 0.0007, 0.0022, 0.0095}, {0.0033, 0.0062, 0.0024, 0.0024, 0.0005, 0.0031, 0.0041, 0.0025, 0.0012, 0.0016, 0.0025, 0.0161, 0.0009, 0.0009, 0.0016, 0.0031, 0.0023, 0.0003, 0.001, 0.0019}, {0.0013, 0.0008, 0.0005, 0.0005, 0.0004, 0.0007, 0.0007, 0.0007, 0.0004, 0.0025, 0.0049, 0.0009, 0.004, 0.0012, 0.0004, 0.0009, 0.001, 0.0002, 0.0006, 0.0023}, {0.0016, 0.0009, 0.0008, 0.0008, 0.0005, 0.0005, 0.0009, 0.0012, 0.0008, 0.003, 0.0054, 0.0009, 0.0012, 0.0183, 0.0005, 0.0012, 0.0012, 0.0008, 0.0042, 0.0026}, {0.0022, 0.001, 0.0009, 0.0012, 0.0004, 0.0008, 0.0014, 0.0014, 0.0005, 0.001, 0.0014, 0.0016, 0.0004, 0.0005, 0.0191, 0.0017, 0.0014, 0.0001, 0.0005, 0.0012}, {0.0063, 0.0023, 0.0031, 0.0028, 0.001, 0.0019, 0.003, 0.0038, 0.0011, 0.0017, 0.0024, 0.0031, 0.0009, 0.0012, 0.0017, 0.0126, 0.0047, 0.0003, 0.001, 0.0024}, {0.0037, 0.0018, 0.0022, 0.0019, 0.0009, 0.0014, 0.002, 0.0022, 0.0007, 0.0027, 0.0033, 0.0023, 0.001, 0.0012, 0.0014, 0.0047, 0.0125, 0.0003, 0.0009, 0.0036}, {0.0004, 0.0003, 0.0002, 0.0002, 0.0001, 0.0002, 0.0003, 0.0004, 0.0002, 0.0004, 0.0007, 0.0003, 0.0002, 0.0008, 0.0001, 0.0003, 0.0003, 0.0065, 0.0009, 0.0004}, {0.0013, 0.0009, 0.0007, 0.0006, 0.0003, 0.0007, 0.0009, 0.0008, 0.0015, 0.0014, 0.0022, 0.001, 0.0006, 0.0042, 0.0005, 0.001, 0.0009, 0.0009, 0.0102, 0.0015}, {0.0051, 0.0016, 0.0012, 0.0013, 0.0014, 0.0012, 0.0017, 0.0018, 0.0006, 0.012, 0.0095, 0.0019, 0.0023, 0.0026, 0.0012, 0.0024, 0.0036, 0.0004, 0.0015, 0.0196}};

struct peptide { std::string seq; int len; float aff; std::vector i; };

std::vector read_IEDB_data() { std::vector iedb_data; std::ifstream iedb_file("data/IEDB_data.tsv"); std::string line; while (getline(iedb_file, line)) { std::stringstream ss(line); std::string sequence; ss >> sequence; if (sequence != "trimmed_seq") { iedb_data.push_back(sequence); } } return iedb_data; }

std::array<std::array<float, 20>, 20> fmatrix_k1() { // Calculates the modified (normalized) blosum62 matrix

int k, j; float marg[20]; float sum;

// initialize margin array for (int i = 0; i < 20; i++) { marg[i] = 0.0; } // initialize k1 for (int i = 0; i < 20; i++) { for (int j = 0; j < 20; j++) { k1[i][j] = 0.0; } } // normalize matrix by marginal frequencies for (j = 0; j < 20; j++) { sum = 0; for (k = 0; k < 20; k++) sum += blm_qij[j][k]; marg[j] = sum; } // calculate K1 for (j = 0; j < 20; j++) { for (k = 0; k < 20; k++) { k1[j][k] = blm_qij[j][k] / (marg[j] * marg[k]); k1[j][k] = pow(k1[j][k], p_beta); } }

return (k1); }

float k3_sum(peptide pep1, peptide pep2) { // Recursively calculate Kernel 3 using Kernel 1 lookups float k2, term, k3 = 0.0; int start1, start2; int k, j1, j2;

float k2_prod_save[31][31][31];

for (k = p_kmin; k <= p_kmax; k++) { for (start1 = 0; start1 <= pep1.len - k; start1++) { for (start2 = 0; start2 <= pep2.len - k; start2++) {

    j1 = pep1.i[start1 + k - 1];
    j2 = pep2.i[start2 + k - 1];
    term = k1[j1][j2];

    if (k == 1) {
      k2 = term;
    } else {
      k2 = k2_prod_save[k - 1][start1][start2] * term;
    }

    k2_prod_save[k][start1][start2] = k2;
    k3 += k2;
  }
}

} return (k3); }

void multi_calc_k3(std::vector peplist1, std::vector peplist2, float threshold) { // Simple method to calculate pairwise TCRMatch scores using two peptide // vectors std::vector<std::tuple<std::string, std::string, float>> results[omp_get_max_threads()];

pragma omp parallel for

for (int i = 0; i < peplist1.size(); i++) { for (int j = 0; j < peplist2.size(); j++) { peptide pep1 = peplist1[i]; peptide pep2 = peplist2[j]; float score = 0.0; score = k3_sum(pep1, pep2) / sqrt(pep1.aff * pep2.aff); if (score > threshold) { int tid = omp_get_thread_num(); results[tid].push_back(make_tuple(pep1.seq, pep2.seq, score)); } } } for (int i = 0; i < omp_get_max_threads(); i++) { for (auto &tuple : results[i]) { std::cout << std::fixed << std::setprecision(2) << std::get<0>(tuple) << " " << std::get<1>(tuple) << " " << std::get<2>(tuple) << std::endl; } } }

// Move this to outside -> import everything you need int main(int argc, char *argv[]) { int opt; int n_threads; float threshold; std::string in_file; int i_flag = -1; int t_flag = -1; int thresh_flag = -1;

// Command line argument parsing while ((opt = getopt(argc, argv, "t:i:s:")) != -1) { switch (opt) { case 't': n_threads = atoi(optarg); t_flag = 1; break; case 'i': in_file = optarg; i_flag = 1; break; case 's': threshold = std::stof(optarg); thresh_flag = 1; break; default: std::cerr << "Usage: ./tcrmatch -i infile_name.txt -t num_threads -s score_threshold" << std::endl; return EXIT_FAILURE; } } // Check that required parameters are there if (i_flag == -1 || t_flag == -1) { std::cerr << "Missing mandatory parameters" << std::endl << "Usage: ./tcrmatch -i infile_name.txt -t num_threads" << std::endl; return EXIT_FAILURE; } if (thresh_flag == -1) { threshold = .97; }

std::vector iedb_data = read_IEDB_data(); std::ifstream file1(in_file); std::string line; std::string alphabet; std::vector peplist1; std::vector peplist2;

omp_set_num_threads(n_threads);

alphabet = "ARNDCQEGHILKMFPSTWYV"; k1 = fmatrix_k1(); while (getline(file1, line)) { std::vector int_vec; for (int i = 0; i < line.length(); i++) { if (alphabet.find(line[i]) == -1) { std::cerr << "Invalid amino acid found in " << line << " at position " << i + 1 << std::endl; return EXIT_FAILURE; } } peplist1.push_back({line, int(line.length()), -99.9, int_vec}); } file1.close();

// Calculate the normalization score (aff) (kernel 3 self vs self) list 1

pragma omp parallel for

for (std::vector::iterator it = peplist1.begin(); it != peplist1.end(); it++) { for (int x = 0; x < it->len; x++) { it->i.push_back(alphabet.find(it->seq[x])); } it->aff = k3_sum(it, it); }

// change to IEDB data for (std::vector::iterator it = iedb_data.begin(); it != iedb_data.end(); it++) { std::vector int_vec; for (int i = 0; i < (it).length(); i++) { if (alphabet.find((it)[i]) == -1) { std::cerr << "Invalid amino acid found in " << it << " at position " << i + 1 << std::endl; return EXIT_FAILURE; } } peplist2.push_back({it, int((*it).length()), -99.9, int_vec}); }

// Calculate the normalization score (aff) (kernel 3 self vs self) for list 2

pragma omp parallel for

for (std::vector::iterator it = peplist2.begin(); it != peplist2.end(); it++) { for (int x = 0; x < it->len; x++) { it->i.push_back(alphabet.find(it->seq[x])); } it->aff = k3_sum(it, it); } multi_calc_k3(peplist1, peplist2, threshold);

return 0; }

[acrinklaw]

So it looks like the code is the same as what I am compiling. And your openMP specification is 4.5 which is also what I used. I think a last step before I do a deep dive into why this might be occurring is to try building without cmake.

Can you try g++ -fopenmp -O3 src/tcrmatch.cpp -o tcrmatch and see if that builds? Then if you do ./tcrmatch you should get Missing mandatory parameters Usage: ./tcrmatch -i infile_name.txt -t num_threads

[tianshilu]

Thank you for your response! I got the same error.

[schristley]

Not sure if it relevant, but to compile on our HPC system here I had set CC and CXX to get cmake to use the right compiler otherwise it kept using the super-old one in /bin

$ module load gcc/9.1.0
$ export CC=/opt/apps/gcc/9.1.0/bin/gcc
$ export CXX=/opt/apps/gcc/9.1.0/bin/g++
$ cmake .
$ cmake --build .
Scanning dependencies of target tcrmatch
[ 50%] Building CXX object CMakeFiles/tcrmatch.dir/src/tcrmatch.cpp.o
[100%] Linking CXX executable tcrmatch
[100%] Built target tcrmatch

$ ./tcrmatch 
Missing mandatory parameters
Usage: ./tcrmatch -i infile_name.txt -t num_threads

[acrinklaw]

Thanks @schristley. That may be the issue. @tianshilu can you verify which version of g++ is being used? g++ --version. If it is using the proper version (9.X) and you still get the error I can do one of two things, I can either provide you with the Python version that has slightly slower run time, or I can provide you with a Dockerfile that I know will run.

[schristley]

If you do a google for "pragma omp parallel for invalid controlling predicate" then you will also find various discussions. It's also possible that openmp doesn't like the the C++ style for iterator, maybe it isn't "basic" enough.

  for (std::vector<peptide>::iterator it = peplist1.begin();

Not sure why it would work for me though

[acrinklaw]

If you do a google for "pragma omp parallel for invalid controlling predicate" then you will also find various discussions. It's also possible that openmp doesn't like the the C++ style for iterator, maybe it isn't "basic" enough.

  for (std::vector<peptide>::iterator it = peplist1.begin();

Not sure why it would work for me though

Yeah that's why I'm confused as well, when I was first writing this it seemed that openMP 4.5 supported iterators as well as the != operator, which it didn't in the past. And I'm having trouble recreating this since it compiles and works fine using a very similar environment

[schristley]

Ah, I bet it's this:

it != peplist1.end();

The != is not a valid operator.

[schristley]

Yeah that's why I'm confused as well, when I was first writing this it seemed that openMP 4.5 supported iterators as well as the != operator, which it didn't in the past. And I'm having trouble recreating this since it compiles and works fine using a very similar environment

Hmm, ok, then it's likely something with the environment...

[acrinklaw]

I have a feeling it is because of g++ versioning. @tianshilu please make sure g++ is up-to-date and 9.X. If this still does not work, email me at acrinklaw@lji.org and I will send you the Python version or Dockerfile, whichever one is easiest for you. Thanks

[tianshilu]

Thank you so much for your responses, suggestions, and help @schristley @acrinklaw. You are totally right. It is the problem of g++ versioning. I am trying to update g++ on my machine.