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scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_range_relax.mpi.linuxgccrelease] Error 1

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scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_range_relax.mpi.linuxgccrelease] Error 1
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Hi there,

An attempt to compile rosetta using a later version of gcc (8.5.0) failed during compilation.(Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting. | RosettaCommons)

I'm not sure if the failure was due to my version of gcc being too high. I have tried to find out whether pyrosetta can be attached to the lib file installed without linking to miniconda3/lib/. The reasons for the failure of the two ways are the same, but the difference is that the app is not completely consistent. The comparison diagram before and after Pyrosetta has been attached. 

(gcx) [ldx022@mn01 source]$ ldd --version
ldd (GNU libc) 2.17
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/N-terminal_acetylation.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_dock.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_mutate_relax.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/idealize_jd2.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/membrane_abinitio2.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/doug_dock_design_min_mod2_cal_cal.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/identify_cdr_clusters.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_dock_setup.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/incorporate_motifs.mpi.linuxgccrelease] Error 1
scons: building terminated because of errors.
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/incorporate_motifs.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_range_relax.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/doug_dock_design_min_mod2_cal_cal.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/hydrate.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/glycan_clash_check.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/helical_bundle_predict.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/ligand_dock.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/mp_lipid_acc.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/ligand_rpkmin.mpi.linuxgccrelease] Error 1
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/grower_prep.mpi.linuxgccrelease] Error 1
scons: building terminated because of errors.
(gcx) [ldx022@mn01 source]$ readelf -Ws /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so | grep aligned_alloc
    51: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND aligned_alloc@GLIBC_2.16 (53)
  3709: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND aligned_alloc@GLIBC_2.16
(gcx) [ldx022@mn01 source]$ readelf -Ws /data/home/ldx022/miniconda3/lib/libstdc++.so | grep aligned_alloc
    51: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND aligned_alloc@GLIBC_2.16 (53)
  3709: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND aligned_alloc@GLIBC_2.16

Any advice would be appreciated !

Regards, 

Lu

 

Category: 
Compilation
Post Situation: 
Unsolved
Sat, 2023-03-11 01:40
ldx022
Top

GLIBC is the plain C standard library (as opposed to the C++ standard library, which is GLIBCXX). The GLIBC version is tied intimately with the kernel and the operating system version. This works normally because the functions in GLIBC are versioned, and newer GLIBC versions have backward-compatible versions for programs compiled on older systems.

However, there's no support on older operating systems for programs which need newer GLIBC versions. That's what your error messages look like to me. You need a newer version of some functions (aligned_alloc@GLIBC_2.16) but your version of the operating system doesn't support them.

It looks like your C++ standard library which you installed with Conda (the /data/home/ldx022/miniconda3/envs/pyro/lib/libstdc++.so) was compiled for a newer operating system. I would have thought that Conda would have checked for the version compatibility when it installed it, but apparently whoever put together that package didn't consider that issue.

Note that it's not the version of the C++ standard library (or the corresponding GCC compiler) which is the issue, it's the version of the operating system on which the pre-build package was compiled. Were you to compile GCC 8.5 yourself on your machine, or were you to find some other GCC Conda package which was built with your OS version in mind, you would probably not have this issue.

Mon, 2023-03-13 07:27
rmoretti
(Reply to #3)
Top 
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libz.so: undefined reference to `memcpy@GLIBC_2.14'
/data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home/ldx022/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'

However, I try to trace the cause of the problem step by step.I first check my environment variables LD_LIBRARY_PATH 

LD_LIBRARY_PATH=/data/home/ldx022/miniconda3/lib/:/data/home/ldx022/software/rosetta.source.release-334/main/source/bin:/data/home/ldx022/miniconda3/lib/:/data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/bin:/data/home/ldx022/software/openmpi-4.1.4/lib:/share/platform/lsf/10.1/linux2.6-glibc2.3-x86_64/lib
ldd -v /data/home/ldx022/miniconda3/lib/libstdc++.so.6
linux-vdso.so.1 =>  (0x00007ffc1ebba000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f929b725000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f929b363000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f929bc58000)
	libgcc_s.so.1 => /data/home/ldx022/miniconda3/lib/libgcc_s.so.1 (0x00007f929b349000)

	Version information:
	/data/home/ldx022/miniconda3/lib/libstdc++.so.6:
		libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
		ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
		libgcc_s.so.1 (GCC_4.2.0) => /data/home/ldx022/miniconda3/lib/libgcc_s.so.1
		libgcc_s.so.1 (GCC_3.4) => /data/home/ldx022/miniconda3/lib/libgcc_s.so.1
		libgcc_s.so.1 (GCC_3.3) => /data/home/ldx022/miniconda3/lib/libgcc_s.so.1
		libgcc_s.so.1 (GCC_3.0) => /data/home/ldx022/miniconda3/lib/libgcc_s.so.1
		libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.6) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.4) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.16) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.17) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
	/lib64/libm.so.6:
		ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
		libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
		libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
	/lib64/libc.so.6:
		ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
		ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
	/data/home/ldx022/miniconda3/lib/libgcc_s.so.1:
		libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
		libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6

According to libc.so.6 (GLIBC_2.17) => /lib64/libc.so.6,I think /data/home/ldx022 miniconda3 / lib/libstdc++. So, this file is linked to 2.17 version of GLIBC successfully,I also checked to see if the GLIBC library /lib64/ libb.so. 6 is available for version 2.17,and the results were positive. 

(gcx) [ldx022@mn01 source]$ strings /lib64/libc.so.6 | grep 2.17
GLIBC_2.17
glibc 2.17
NPTL 2.17
GNU C Library (GNU libc) stable release version 2.17, by Roland McGrath et al.
GLIBC_2.17
libc-2.17.so.debug

Then I try to find /data/home/ldx022 / miniconda3 / envs/GCX/bin /.. / lib/GCC/x86_64 conda - - the gnu/Linux 8.5.0 /.. /.. /.. /.. /x86_64-conda-linux-gnu/bin/ld searching path， 

(gcx) [ldx022@mn01 source]$ /data/home/ldx022/miniconda3/envs/gcx/bin/../lib/gcc/x86_64-conda-linux-gnu/8.5.0/../../../../x86_64-conda-linux-gnu/bin/ld --verbose | grep SEARCH
SEARCH_DIR("=/home/conda/feedstock_root/build_artifacts/binutils_split_1674833318037/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/x86_64-conda-linux-gnu/lib64"); SEARCH_DIR("=/home/conda/feedstock_root/build_artifacts/binutils_split_1674833318037/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib64"); SEARCH_DIR("=/usr/local/lib64"); SEARCH_DIR("=/lib64"); SEARCH_DIR("=/usr/lib64"); SEARCH_DIR("=/home/conda/feedstock_root/build_artifacts/binutils_split_1674833318037/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/x86_64-conda-linux-gnu/lib"); SEARCH_DIR("=/home/conda/feedstock_root/build_artifacts/binutils_split_1674833318037/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib"); SEARCH_DIR("=/usr/local/lib"); SEARCH_DIR("=/lib"); SEARCH_DIR("=/usr/lib");

SEARCH_DIR("=/lib64") shows that the directory /lib64 is in the ld search range.But trying to compile again and again it was unsuccessful. Keeps returning the mistake at the beginning of my comment. I can't figure out what went wrong.

But the amazing thing is that when I added /lib64 to LD_LIBRARY_PATH, the compilation worked!The new LD_LIBRARY_PATH is that : 

LD_LIBRARY_PATH=/lib64:/data/home/ldx022/miniconda3/lib/:/data/home/ldx022/software/rosetta.source.release-334/main/source/bin:/data/home/ldx022/miniconda3/lib/:/data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/bin:/data/home/ldx022/software/openmpi-4.1.4/lib:/share/platform/lsf/10.1/linux2.6-glibc2.3-x86_64/lib

I still can't figure out before I add /lib64 to LD_LIBRARY_PATH,the gcx ld search directory in the conda environment already includes /lib64 (as shown above),why it failed to compile. Why does adding /lib64 work?

But when I ran antibody.mpi.linuxgccrelease,it still shows 

antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by antibody.mpi.linuxgccrelease)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols.8.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols.7.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols.7.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols.7.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_e.6.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_e.6.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_e.6.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_d.6.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_d.6.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_d.6.so)
antibody.mpi.linuxgccrelease: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data/home/ldx022/software/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8.5/mpi/libprotocols_c.6.so)

These high version of the GLIBCXX and CXXABI indeed couldn't find in/lib64/libstdc++.so.6, but it can be found in /data/home/ldx022 miniconda3 / lib/libstdc++. So. 6.

I guess the problem seems to be that I can't link /lib64 to /data/home/ldx022/miniconda3/lib/libstdc++.so.6 successfully.What should I do？

Mon, 2023-03-20 02:31
ldx022