Comments (7)
Maybe we can compile Uni-Dock using older glibc version to solve this problem and similar problem on CentOS with old versions. @caic99
from uni-dock.
Hi,
it's not so simple to upgrade the gcc...usually this means the risk to break something is high.
By the way I managed to workaround by following this answer https://stackoverflow.com/a/61738375.
I downloaded two rpm (libstdc++-11.3.1-4.3.el9.x86_64.rpm and glibc-2.34-68.el9.x86_64.rpm) and extracted by rpm2cpio in a private local folder. Now the program is running.
from uni-dock.
Hi @andreacarotti331 ,
Would you try installing gcc-9 to match the glibc version? The exetutable is compiled using gcc 9.4.0, fyi.
from uni-dock.
I think it would be better if you don't prove the source code.
You have two option:
- compile with static libraries so it will be "release independent" , but you have to check if the performances are mantained
- compile with older glibc version and create different unidock binaries...
My bests
Andrea
from uni-dock.
Hi, got the same issue here
from uni-dock.
We have compiled Uni-Dock with glibc 2.17.
unidock_glibc2_17.zip
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Hi, this 2.17 build brings up more dependencies I don't have. I checked this with ldd unidock_glibc2_17
:
$ ldd unidock_glibc2_17
linux-vdso.so.1 (0x00007fffc491f000)
libboost_system.so.1.77.0 => not found
libboost_thread.so.1.77.0 => not found
libboost_serialization.so.1.77.0 => not found
libboost_filesystem.so.1.77.0 => not found
libboost_program_options.so.1.77.0 => not found
libboost_chrono.so.1.77.0 => not found
libboost_atomic.so.1.77.0 => not found
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f317c2bb000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f317c078000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f317be70000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f317bc6c000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f317b85f000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f317b4c1000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f317b2a9000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f317aeb8000)
/lib64/ld-linux-x86-64.so.2 (0x00007f317c4da000)
Please have a look at the missing dependencies starting with libboost*. I have 1.65 on the system but not 1.77. Are those dependencies really needed? I don't see them in the original binary build
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Related Issues (20)
- 1.1.1 source release contains version string 1.1.0 HOT 1
- Error in vina score HOT 2
- typo in examples HOT 1
- missing installation instruction in unidock_tools
- How to dock
- WARNING: Could not find any conformations
- run unidock, report segmentation fault while using file index
- OOM using ad4 scoring function
- CUDA Runtime Error when using ad4 maps HOT 4
- Fail on screening test case mmp13 on version v1.1.x HOT 2
- Unidock pipeline fails to read ligand index HOT 1
- target_compile_features no known features for CXX compiler HOT 6
- Unknown order of ligands in the output HOT 2
- in ligand index, unable to find mol file, only first without others. HOT 1
- Seed doesn't seem to be working properly. HOT 3
- Cuda runtime error =
- MCDock Run Rigid Docking with Incorrect Input SDF Files
- How to get score when run unidock tooks? HOT 4
- cmake -B build -D FETCH_BOOST=ON does not fetch boost HOT 6
- Compiling error on CUDA 11
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