Member Site › Forums › Rosetta 3 › Rosetta 3 – Build/Install › error in installing rosetta in ubuntu64
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May 12, 2021 at 1:44 am #3767
Anonymous
Hi, sorry for disturbing you but I have problems installing Rosetta
Could someone help me, please?
regards
hr
tar -xvzf rosetta_src_2021.16.61629_bundle.tgz
ubuntu@ubuntu:~/software1$ python -V
Python 2.7.18
ubuntu@ubuntu:~/software1$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v –with-pkgversion=’Ubuntu 10.2.0-5ubuntu1~20.04′ –with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs –enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 –prefix=/usr –with-gcc-major-version-only –program-suffix=-10 –program-prefix=x86_64-linux-gnu- –enable-shared –enable-linker-build-id –libexecdir=/usr/lib –without-included-gettext –enable-threads=posix –libdir=/usr/lib –enable-nls –enable-clocale=gnu –enable-libstdcxx-debug –enable-libstdcxx-time=yes –with-default-libstdcxx-abi=new –enable-gnu-unique-object –disable-vtable-verify –enable-plugin –enable-default-pie –with-system-zlib –enable-libphobos-checking=release –with-target-system-zlib=auto –enable-objc-gc=auto –enable-multiarch –disable-werror –with-arch-32=i686 –with-abi=m64 –with-multilib-list=m32,m64,mx32 –enable-multilib –with-tune=generic –enable-offload-targets=nvptx-none=/build/gcc-10-WJNXnb/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-WJNXnb/gcc-10-10.2.0/debian/tmp-gcn/usr,hsa –without-cuda-driver –enable-checking=release –build=x86_64-linux-gnu –host=x86_64-linux-gnu –target=x86_64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 10.2.0 (Ubuntu 10.2.0-5ubuntu1~20.04)
ubuntu@ubuntu:~/software1/rosetta_src_2021.16.61629_bundle/main/source$ ./scons.py -j 20 mode=release bin
scons: Reading SConscript files …
Copy(“user.options”, “user.options.template”)
Copy(“user.settings”, “user.settings.template”)
Copy(“/home/ubuntu/software1/rosetta_src_2021.16.61629_bundle/main/source/src/pilot_apps.src.settings”, “/home/ubuntu/software1/rosetta_src_2021.16.61629_bundle/main/source/src/pilot_apps.src.settings.template”)
Running versioning script … Release package detected, using rosetta/main/.release.json to acquire version information…
Done. (0.0 seconds)
file ./options.dox being updated
file ./full-options-list.md being updated
Number of option files updated: 2
Total 4580 options.
Finished updating ResidueProperty code
— no changes needed
Finished updating VariantType code
— no changes needed
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/apps/public/AbinitioRelax.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/AbinitioRelax.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/devel/init.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/init.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/init.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/init.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register1.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register1.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register2.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register2.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register3.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register3.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register4.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register4.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/AddorRemoveCsts.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/AddorRemoveCsts.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/BackboneSampler.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/BackboneSampler.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/DesignVsNativeComparison.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/DesignVsNativeComparison.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/enzdes_util.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/enzdes_util.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesBaseProtocol.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesBaseProtocol.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesFixBBProtocol.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesFixBBProtocol.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesFlexBBProtocol.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesFlexBBProtocol.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesJobInputter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesJobInputter.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesJobOutputter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesJobOutputter.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesMovers.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesMovers.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesTaskOperations.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesTaskOperations.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzFilters.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzFilters.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzRepackMinimize.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzRepackMinimize.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register1.os] Error 1
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register3.os] Error 1
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/DesignVsNativeComparison.os] Error 1
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/AddorRemoveCsts.os] Error 1
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesBaseProtocol.os] Error 1
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register4.os] Error 1
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/enzdes_util.os] Error 1
scons: building terminated because of errors.
I used these methods, too:gcc 9.3,rosetta_bin_linux_3.12_bundle.tgz,ubuntu-20.04.1-desktop-amd64.iso,
and the method in https://www.rosettacommons.org/node/add/forum/53 ,as follows
A third option, if you’re comfortable editing the source files, would be to simply delete the `using std::string;` lines from source/src/core/io/silent/SilentStruct.cc (it turns out they’re unneeded.) You may also need to delete the `using build::BuildInstructionOP;` line from source/src/protocols/forge/remodel/RemodelWorkingSet.cc — There are some other fixes included in the developers’ version, but I think those should be sufficient to get you a working version with GCC1
but I thied these mothods but also did not work.
Could someone help me, please?
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May 12, 2021 at 1:50 am #15894
Hello,
I cannot be sure but I believe that your problem may be that you are running out of memory!
Try a smaller j in your scons command such as:
./scons.py -j 4 mode=release bin
When you use too much memory linux will kill whatever is hogging the most memory so you can just -j 1, -j 4, -j 10, etc and hopefully one will work.
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May 13, 2021 at 12:46 am #15895
Thank you, danpf
it did not work , I have installed VMware-workstation-full-15.0.2-10952284.exe, memory is 2GB
ubuntu@ubuntu:~/software1/rosetta_src_2021.16.61629_bundle/main/source$ ./scons.py -j 4 mode=release bin
scons: Reading SConscript files …
Running versioning script … Release package detected, using rosetta/main/.release.json to acquire version information…
Done. (0.0 seconds)
file ./options.dox being updated
file ./full-options-list.md being updated
Number of option files updated: 2
Total 4580 options.
Finished updating ResidueProperty code
— no changes needed
Finished updating VariantType code
— no changes needed
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register1.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register1.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register3.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register3.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register4.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register4.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/AddorRemoveCsts.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/AddorRemoveCsts.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/DesignVsNativeComparison.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/DesignVsNativeComparison.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/enzdes_util.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/enzdes_util.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++ -o build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/enzdes/EnzdesBaseProtocol.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/10 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/enzdes/EnzdesBaseProtocol.cc
g++: warning: switch ‘-ffor-scope’ is no longer supported
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
scons: *** [build/src/release/linux/5.8/64/x86/gcc/10/default/protocols/init/register4.os] Error 1
scons: building terminated because of errors.
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May 13, 2021 at 3:15 am #15896
Hello,
2GB of memory is not very much. I am not sure what the minimum required to install rosetta is, but that seems close to the limit.
Could you try -j 1 and let me know if that works?
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May 13, 2021 at 3:18 am #15897
I do not know much about Windows, but I have heard that WSL (windows subsystem for linux) is an alternative to installing a full ubuntu operating system under vmware. If you look into that I think you may be able to install Rosetta utilizing more of your system’s resources.
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May 13, 2021 at 3:29 am #15898
I had install a full ubuntu operating system under vmware,and tried ./scons.py -j 1 mode=release bin,but it had the same error as above.
Thank you,danpf
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May 13, 2021 at 3:38 pm #15901
Hello,
I talked with some other members in the community and we believe that 2GB of memory might not be enough to compile rosetta.
As an alternative you may be able to download the static binaries from the download site (they are already compiled for you) but they are quite large in size (i believe 44GB unzipped, 16 GB zipped — so you will need at least ~80GB of free disk space to download and unzip them).
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May 14, 2021 at 7:44 am #15902
Thank you,I will try the static binaries.
I’ll ask you for advice when I have problems
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