Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output: Change Dir: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_03e1c/fast && /usr/bin/gmake -f CMakeFiles/cmTC_03e1c.dir/build.make CMakeFiles/cmTC_03e1c.dir/build gmake[1]: Entering directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_03e1c.dir/src.c.o /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -DCMAKE_HAVE_LIBC_PTHREAD -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -std=gnu99 -o CMakeFiles/cmTC_03e1c.dir/src.c.o -c /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp/src.c Linking C executable cmTC_03e1c /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_03e1c.dir/link.txt --verbose=1 /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -L/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/rlwoltz/anaconda3/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/lib -L/home/rlwoltz/anaconda3/lib CMakeFiles/cmTC_03e1c.dir/src.c.o -o cmTC_03e1c /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/cmTC_03e1c.dir/src.c.o: in function `main': src.c:(.text.startup.main+0x24): undefined reference to `pthread_create' /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: src.c:(.text.startup.main+0x2e): undefined reference to `pthread_detach' /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: src.c:(.text.startup.main+0x38): undefined reference to `pthread_cancel' /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: src.c:(.text.startup.main+0x44): undefined reference to `pthread_join' /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: src.c:(.text.startup.main+0x50): undefined reference to `pthread_atfork' collect2: error: ld returned 1 exit status gmake[1]: *** [CMakeFiles/cmTC_03e1c.dir/build.make:99: cmTC_03e1c] Error 1 gmake[1]: Leaving directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' gmake: *** [Makefile:127: cmTC_03e1c/fast] Error 2 Source file was: #include static void* test_func(void* data) { return data; } int main(void) { pthread_t thread; pthread_create(&thread, NULL, test_func, NULL); pthread_detach(thread); pthread_cancel(thread); pthread_join(thread, NULL); pthread_atfork(NULL, NULL, NULL); pthread_exit(NULL); return 0; } Determining if the function pthread_create exists in the pthreads failed with the following output: Change Dir: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_152f8/fast && /usr/bin/gmake -f CMakeFiles/cmTC_152f8.dir/build.make CMakeFiles/cmTC_152f8.dir/build gmake[1]: Entering directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_152f8.dir/CheckFunctionExists.c.o /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -DCHECK_FUNCTION_EXISTS=pthread_create -std=gnu99 -o CMakeFiles/cmTC_152f8.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.22/Modules/CheckFunctionExists.c Linking C executable cmTC_152f8 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_152f8.dir/link.txt --verbose=1 /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -DCHECK_FUNCTION_EXISTS=pthread_create -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -L/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/rlwoltz/anaconda3/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/lib -L/home/rlwoltz/anaconda3/lib CMakeFiles/cmTC_152f8.dir/CheckFunctionExists.c.o -o cmTC_152f8 -lpthreads /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lpthreads: No such file or directory collect2: error: ld returned 1 exit status gmake[1]: *** [CMakeFiles/cmTC_152f8.dir/build.make:99: cmTC_152f8] Error 1 gmake[1]: Leaving directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' gmake: *** [Makefile:127: cmTC_152f8/fast] Error 2 Performing C SOURCE FILE Test CMath_LINKS_WITHOUT_M failed with the following output: Change Dir: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_24f15/fast && /usr/bin/gmake -f CMakeFiles/cmTC_24f15.dir/build.make CMakeFiles/cmTC_24f15.dir/build gmake[1]: Entering directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_24f15.dir/src.c.o /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -DCMath_LINKS_WITHOUT_M -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -fPIE -std=gnu99 -o CMakeFiles/cmTC_24f15.dir/src.c.o -c /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp/src.c Linking C executable cmTC_24f15 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_24f15.dir/link.txt --verbose=1 /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -L/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/rlwoltz/anaconda3/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/lib -L/home/rlwoltz/anaconda3/lib CMakeFiles/cmTC_24f15.dir/src.c.o -o cmTC_24f15 /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/cmTC_24f15.dir/src.c.o: in function `main': src.c:(.text.startup.main+0x10): undefined reference to `sin' collect2: error: ld returned 1 exit status gmake[1]: *** [CMakeFiles/cmTC_24f15.dir/build.make:99: cmTC_24f15] Error 1 gmake[1]: Leaving directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' gmake: *** [Makefile:127: cmTC_24f15/fast] Error 2 Source file was: #include int main(int argc, char** argv) { return sin(argc - 1); } Determining if the function arsecond exists in the library failed with the following output: Change Dir: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_942c6/fast && /usr/bin/gmake -f CMakeFiles/cmTC_942c6.dir/build.make CMakeFiles/cmTC_942c6.dir/build gmake[1]: Entering directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' Building Fortran object CMakeFiles/cmTC_942c6.dir/TryLinkLibrary.F90.o /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gfortran -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -fPIE -c /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp/TryLinkLibrary.F90 -o CMakeFiles/cmTC_942c6.dir/TryLinkLibrary.F90.o Linking Fortran executable cmTC_942c6 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_942c6.dir/link.txt --verbose=1 /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gfortran -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/envs/AmberTools22/lib -L/home/rlwoltz/anaconda3/envs/AmberTools22/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/rlwoltz/anaconda3/lib -Wl,-rpath-link,/home/rlwoltz/anaconda3/lib -L/home/rlwoltz/anaconda3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include CMakeFiles/cmTC_942c6.dir/TryLinkLibrary.F90.o -o cmTC_942c6 /home/rlwoltz/anaconda3/envs/AmberTools22/lib/libarpack.so /home/rlwoltz/anaconda3/envs/AmberTools22/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: CMakeFiles/cmTC_942c6.dir/TryLinkLibrary.F90.o: in function `main': TryLinkLibrary.F90:(.text.startup.main+0x20): undefined reference to `arsecond_' collect2: error: ld returned 1 exit status gmake[1]: *** [CMakeFiles/cmTC_942c6.dir/build.make:100: cmTC_942c6] Error 1 gmake[1]: Leaving directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' gmake: *** [Makefile:127: cmTC_942c6/fast] Error 2 Determining if the Perl module Chemistry::Mol exists failed with the following error output: Can't locate Chemistry/Mol.pm in @INC (you may need to install the Chemistry::Mol module) (@INC contains: /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl/mm_pbsa /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/5.32/site_perl /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/site_perl /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/5.32/vendor_perl /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/vendor_perl /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/5.32/core_perl /home/rlwoltz/anaconda3/envs/AmberTools22/lib/perl5/core_perl .) at -e line 1. BEGIN failed--compilation aborted at -e line 1. Determining if the include file Windows.h exists failed with the following output: Change Dir: /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_53da6/fast && /usr/bin/gmake -f CMakeFiles/cmTC_53da6.dir/build.make CMakeFiles/cmTC_53da6.dir/build gmake[1]: Entering directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_53da6.dir/CheckIncludeFile.c.o /home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rlwoltz/anaconda3/envs/AmberTools22/include -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -fcommon -std=gnu99 -o CMakeFiles/cmTC_53da6.dir/CheckIncludeFile.c.o -c /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c /home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c:1:10: fatal error: Windows.h: No such file or directory 1 | #include | ^~~~~~~~~~~ compilation terminated. gmake[1]: *** [CMakeFiles/cmTC_53da6.dir/build.make:78: CMakeFiles/cmTC_53da6.dir/CheckIncludeFile.c.o] Error 1 gmake[1]: Leaving directory '/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp' gmake: *** [Makefile:127: cmTC_53da6/fast] Error 2