Hello all:
I am trying to compile a parallel version of Amber.
I first downloaded amber18 and ambertools20 and performed the serial compilation.
Next, I wanted to compile the parallel version.
I went to $AMBERHOME/AmberTools/src and issued ./configure_mpich gnu.
That went fine only some warnings.
Next I went back to $AMBERHOME and issued ./configure -mpi gnu.
Here is where I get my error. Please see the output:
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 20 patches:
No patches available
Available Amber 20 patches:
update.1, update.2, update.3, update.4, update.5, update.6, update.7, update.8, update.9, update.10,update.11
There are patches available. Do you want to apply them now? [y/N] (Recommended Y)
N
NOT updating your tree and continuing anyway.
AMBER_PREFIX=/usr/local/amber/amber18/
AMBER_SOURCE=/usr/local/amber/amber18/
Using the AmberTools miniconda installation in /usr/local/amber/amber18//miniconda
version 3.8.5
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
The C version is 4.8.5
The Fortran version is 9.3.0
Testing the gcc compiler:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the g++ compiler:
g++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Testing bison: OK
Checking NetCDF...
Using bundled NetCDF library.
Using existing NetCDF in '/usr/local/amber/amber18/'
Checking for zlib: OK
Checking for libbz2: OK
Configuring fftw-3.3 (may be time-consuming)...OK
Compiling the FFTW3 interface (may be time-consuming)...OK
Configuring boost (may be time-consuming)...OK
Compiling boost (may be time-consuming)...OK
Configuring CPPTRAJ...
CPPTRAJ configure failed. Check '/usr/local/amber/amber18/AmberTools/src/cpptraj_config.log' for details.
Configure failed due to the errors above!
(amber) [amber18]$ more /usr/local/amber/amber18/AmberTools/src/cpptraj_config.log
fftw3 enabled.
fftw3 specified: /usr/local/amber/amber18/
sanderlib disabled.
netcdf specified: /usr/local/amber/amber18/
blas specified: /usr/local/amber/amber18/
lapack specified: /usr/local/amber/amber18/
arpack specified: /usr/local/amber/amber18/
Testing basic C++11 support: Not present
Testing fix for STDIO/MPI ordering:
Error: Test compile failed: mpicxx -Wall -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -o testp testp.cpp
Error: Check the output below for error messages:
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: warning: librt.so.1, needed by /usr/local/amber/amber18/lib/libmpicxx.so, not found (try using -rpath or -rpath-link)
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: warning: libpthread.so.0, needed by /usr/local/amber/amber18/lib/libmpicxx.so, not found (try using -rpath or -rpath-link)
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: warning: libgfortran.so.5, needed by /usr/local/amber/amber18/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `aio_error64.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `pthread_mutexattr_setpshared.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `aio_suspend64.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `clock_getres.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `pthread_mutexattr_init.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `pthread_mutexattr_destroy.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `aio_write64.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `clock_gettime.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `aio_return64.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `pthread_create.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `pthread_mutexattr_settype.GLIBC_2.2.5'
/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: /usr/local/amber/amber18/lib/libmpi.so: undefined reference to `aio_read64.GLIBC_2.2.5'
I confirmed that librt.so.1, libpthread.so.0 and libgfortran.so.5 are present on my system and are also accessible through the LD_LIBRARY_PATH variable.
I am not sure how to proceed. Any pointers from you are greatly appreciated?
Best wishes,
Markus
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Received on Wed Apr 28 2021 - 12:30:03 PDT
