Fix buffer overflows http://www.mothur.org/forum/viewtopic.php?f=4&t=591 --- Mothur.source/filterseqscommand.cpp +++ Mothur.source/filterseqscommand.cpp @@ -305,8 +305,8 @@ //wait on chidren for(int i = 1; i < processors; i++) { - char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); } }else { //you are a child process @@ -326,11 +326,11 @@ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } - char buf[4]; + char buf[5]; strcpy(buf, "done"); //tell parent you are done. - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } MPI_File_close(&outMPI); --- Mothur.source/distancecommand.cpp +++ Mothur.source/distancecommand.cpp @@ -271,8 +271,8 @@ for(int i = 1; i < processors; i++) { if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; } - char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); } }else { //you are a child process //do your part @@ -280,10 +280,10 @@ if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; } - char buf[4]; + char buf[5]; strcpy(buf, "done"); //tell parent you are done. - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } MPI_File_close(&outMPI); --- Mothur.source/chimeracheckcommand.cpp +++ Mothur.source/chimeracheckcommand.cpp @@ -269,8 +269,8 @@ //wait on chidren for(int j = 1; j < processors; j++) { - char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -288,9 +288,9 @@ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } //tell parent you are done. - char buf[4]; + char buf[5]; strcpy(buf, "done"); - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } //close files