Dear Community,
I originally had amber18 installed on ubuntu 20 LTS and
upgraded to Ubuntu Jellyfish which has come with a series of issues (xorg
not default and libraries not being there) this broke amber18 due to
gfortran being upgraded from the one used to install amber18. I've decided
to use the opportunity to upgrade to Amber22 at the same time but I'm
running into a lot of errors which I think is coming from differences in
the new ubuntu jellyfish. While I've fought through many of these issues,
I'm still having one major one which is that amber can't seem to find
windows.h files when running run_cmake.
Some key things I've done so far:
- force ubuntu to use xorg (not the new default which doesn't allow screen
sharing). This seem to solve amber failure to install with GUI.
-changed the header of file
amber22_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh
from #!/bin/sh -> #!/bin/bash
the file fails if it is run in sh script.
Any suggestions on how to get past this windows.h missing file? is it
really looking for a windows OS file or is this more of a gui window file?
I don't need this to be compatible with windows at all. Has anyone
successfully installed Amber22 on Jellyfish using the run_cmake file? What
steps did you need to make? Should I just revert to the former way of
installation?
Thank you,
Ryan
Here is the error log:
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
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/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 <pthread.h>
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 &&
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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
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/home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona
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-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
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/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
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/home/rlwoltz/anaconda3/envs/AmberTools22/bin/gcc -march=nocona
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/home/rlwoltz/anaconda3/envs/AmberTools22/include -Wl,-O2
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/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 <math.h>
int main(int argc, char** argv)
{
return sin(argc - 1);
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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
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gmake[1]: Entering directory
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Building Fortran object CMakeFiles/cmTC_942c6.dir/TryLinkLibrary.F90.o
/home/rlwoltz/anaconda3/envs/AmberTools22/bin/gfortran -march=nocona
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/home/rlwoltz/anaconda3/envs/AmberTools22/include -fPIE -c
/home/rlwoltz/protein_modeling/amber22_src/build/CMakeFiles/CMakeTmp/TryLinkLibrary.F90
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Linking Fortran executable cmTC_942c6
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_942c6.dir/link.txt
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/home/rlwoltz/anaconda3/envs/AmberTools22/bin/gfortran -Wl,-O2
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-Wl,-rpath-link,/home/rlwoltz/anaconda3/envs/AmberTools22/lib
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-Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags
-Wl,--gc-sections -Wl,-rpath,/home/rlwoltz/anaconda3/lib
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/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
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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
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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 <Windows.h>
| ^~~~~~~~~~~
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
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Received on Thu Dec 29 2022 - 15:00:02 PST
