One problem with the initial use of antibody application is that there is complie issue shown as the following:
[ ERROR ] : Caught exception : File: src/protocols/antibody/grafting/regex_based_cdr_detection.cc :47 [ ERROR ] UtilityExitException EROREROR: Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting.
According to the discussion on this issue in the forum, I learned that it was caused by the low version of gcc (the original version of gcc was 4.8).
Due to permissions, I can only update the gcc in the conda environment. Install gcc 8.4.0 (the lowest available, see Figure 1 for compiler versions in conda environment,The following operations are done in this conda environment) in conda environment, remove openmpi and compile openmpi from scratch, using the commands as follows:
tar -zxvf /data/home/ldx022/software/openmpi-4.1.4.tar.gz cd /data/home/ldx022/software/openmpi-4.1.4.tar.gz ./configure -prefix=/data/home/ldx022/software/openmpi-4.1.4 make -j 4 make install
Then start clean with the the "./scons.py -c mode=release bin extras=mpi" command (I also tried uninstalling rosetta from scratch earlier).
Compile from scratch with the "./scons.py -j 40 mode=release bin extras=mpi" command. In the rosetta folder, the build file in source is still 4.8 gcc(/data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/mpi), plus a new problem as the figure 2.
I couldn't find the libcifparse.so file it wanted, so I found the required libcifparse.so file in rosetta in another user's directory and put it in /data/home/ldx022/lib.
Then I added "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/data/home/ldx022/lib" to the .bashrc file and source it, as a result:
gcc/4.8/mpi/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/RcsbFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/mpi -Lexternal -Lbin -L/share/platform/lsf/10.1/linux2.6-glibc2.3-x86_64/lib -L/data/home/ldx022/lib -L/usr/lib -L/usr/local/lib /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/cifparse/CifScanner.os: unrecognized relocation (0x2a) in section `.text' /usr/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status scons: *** [build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/libcifparse.so] Error 1 scons: building terminated because of errors.
The current problems are:
1. Is there any solution to the above situation ( compiler versions in conda environment are shown in figure 1)
2. Should I use a more advanced version of g++? I have already used the "https://www.rosettacommons.org/docs/latest/build_documentation/Cxx11Support" where it provides a test script, the result is shown in figure 3, The failure of option test seems very important to me, but since I can only use conda, I found that g++ could not be found in conda by using conda search, only mpicc and mpicxx are not high, I wonder whether they can meet the requirements.
(123) [ldx022@mn01 ~]$ conda search g++ Loading channels: done No match found for: g++. Search: *g++* PackagesNotFoundError: The following packages are not available from current channels: - g++ Current channels: - https://repo.anaconda.com/pkgs/main/linux-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. (123) [ldx022@mn01 ~]$ conda search mpiCC Loading channels: done No match found for: mpicc. Search: *mpicc* # Name Version Build Channel mpich-mpicc 3.2.1 h7b6447c_8 pkgs/main mpich-mpicc 3.3.2 hf39692e_0 pkgs/main openmpi-mpicc 4.0.2 h7b6447c_1 pkgs/main (123) [ldx022@mn01 ~]$ conda search mpicxx Loading channels: done No match found for: mpicxx. Search: *mpicxx* # Name Version Build Channel mpich-mpicxx 3.2.1 hfd86e86_8 pkgs/main mpich-mpicxx 3.3.2 h7b6447c_0 pkgs/main openmpi-mpicxx 4.0.2 hfd86e86_1 pkgs/main (123) [ldx022@mn01 ~]$ conda search mpicc Loading channels: done No match found for: mpicc. Search: *mpicc* # Name Version Build Channel mpich-mpicc 3.2.1 h7b6447c_8 pkgs/main mpich-mpicc 3.3.2 hf39692e_0 pkgs/main openmpi-mpicc 4.0.2 h7b6447c_1 pkgs/main
3. I am a novice, so I don't know if I compiled openmpi correctly. I compiled openmpi in a conda environment (manually rm the previous openmpi folder before recompiling, and rosetta did a similar thing when recompiling). gcc in this environment is version 8.4.0, but the final compilation of rosetta in this environment still shows version 4.8. What can I do？
I've tried many things, but nothing has worked. What should I do?
Because this is very important to me, so I am a little anxious.Any advice would be appreciated!