:/mnt/c/amber/amber20_src/build$ ./run_cmake
-- **************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.16.3
-- For how to use this build system, please read this wiki:
--     http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--     http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Amber source not found, only building AmberTools
-- Found MPI_C: /mnt/c/amber/amber20/lib/libmpi.so (found version "4.0")
-- Found MPI_CXX: /mnt/c/amber/amber20/lib/libmpicxx.so (found version "4.0")
-- Found MPI_Fortran: /mnt/c/amber/amber20/lib/libmpifort.so (found version "4.0")
-- Found MPI: TRUE (found version "4.0")
-- MPI C Compiler: /mnt/c/amber/amber20/bin/mpicc
-- MPI CXX Compiler: /mnt/c/amber/amber20/bin/mpicxx
-- MPI Fortran Compiler: /mnt/c/amber/amber20/bin/mpif90
-- If these are not the correct MPI wrappers, then set MPI_<language>_COMPILER to the correct wrapper and reconfigure.
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Miniconda is installed in the build directory!
-- Found perl make: /usr/bin/make
-- Perl modules well be installed to AMBERHOME/lib/perl
-- Running updater...
-- >>> Preparing to apply updates... please wait.
-- >>> No new updates available for AmberTools 21
-- Updater done.  If you want to install updates, then set the APPLY_UPDATES variable to true.
-- Checking whether to use built-in libraries...
-- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY READLINE_WORKS)
-- Unable to locate MKL_HOME for your system.  To use MKL, set MKL_HOME to point to your MKL installation location.
-- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP_Fortran: -fopenmp
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY MKL_WORKS MKL_FORTRAN_WORKS)
-- Cannot search for FFTW Fortran headers because the serial headers were not found
-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS FFTW_LIBRARY_MPI FFTW_INCLUDES_MPI FFTW_MPI_WORKS)
-- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND)
-- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND)
-- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES)
-- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS)
-- A library with BLAS API not found. Please specify library location.
-- LAPACK requires BLAS
-- A library with LAPACK API not found. Please specify library location.
-- The ARPACK library was not found.  Please set ARPACK_LIBRARY to point to it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
-- Could NOT find PnetCDF (missing: PnetCDF_LIBRARY PnetCDF_INCLUDE_DIR PnetCDF_WORKS)
-- Could not find some or all of the five main APBS libraries. Please set APBS_GENERIC_LIB, APBS_ROUTINES_LIB,
APBS_PMGC_LIB, APBS_MG_LIB, and APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES)
-- Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
-- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS)
-- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY LIO_WORKS)
-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
-- Checking for Python package mpi4py -- not found
-- Checking for perl module Chemistry::Mol
-- Checking for perl module Chemistry::Mol - found at /mnt/c/amber/amber20/lib/perl/Chemistry/Mol.pm
-- Found PerlModules: TRUE
-- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system program_options iostreams regex timer chrono filesystem graph)
-- Could NOT find MBX (missing: MBX_DIR)
-- Could not find MBX.  To locate it, add its install dir to the prefix path.
-- Could NOT find tng_io (missing: tng_io_DIR)
-- Could not find tng_io.  To locate it, add its install dir to the prefix path.
-- Cannot find PLUMED.  You will still be able to load it at runtime.  If you want to link it at build time, set PLUMED_ROOT to where you installed it.
-- Generating amber source scripts
-- Configuring subdirs...
-- Check size of MPI_Fint
-- Check size of MPI_Fint - done
-- FFTW: compiler supports stack alignment: TRUE
-- Found bash: /usr/bin/bash
-- netcdf-fortran: Detected TS29113 support in Fortran compiler
-- Looking for MPI_MODE_RDWR
-- Looking for MPI_MODE_RDWR - found
-- Looking for MPI_COMBINER_DUP
-- Looking for MPI_COMBINER_DUP - not found
-- Looking for MPI_COMBINER_DUP as #define or enum
-- Looking for MPI_COMBINER_DUP as #define or enum - found
-- Looking for MPI_COMBINER_HVECTOR_INTEGER
-- Looking for MPI_COMBINER_HVECTOR_INTEGER - not found
-- Looking for MPI_COMBINER_HVECTOR_INTEGER as #define or enum
-- Looking for MPI_COMBINER_HVECTOR_INTEGER as #define or enum - found
-- Looking for MPI_COMBINER_HINDEXED_INTEGER
-- Looking for MPI_COMBINER_HINDEXED_INTEGER - not found
-- Looking for MPI_COMBINER_HINDEXED_INTEGER as #define or enum
-- Looking for MPI_COMBINER_HINDEXED_INTEGER as #define or enum - found
-- Looking for MPI_COMBINER_SUBARRAY
-- Looking for MPI_COMBINER_SUBARRAY - not found
-- Looking for MPI_COMBINER_SUBARRAY as #define or enum
-- Looking for MPI_COMBINER_SUBARRAY as #define or enum - found
-- Looking for MPI_COMBINER_DARRAY
-- Looking for MPI_COMBINER_DARRAY - not found
-- Looking for MPI_COMBINER_DARRAY as #define or enum
-- Looking for MPI_COMBINER_DARRAY as #define or enum - found
-- Looking for MPI_COMBINER_RESIZED
-- Looking for MPI_COMBINER_RESIZED - not found
-- Looking for MPI_COMBINER_RESIZED as #define or enum
-- Looking for MPI_COMBINER_RESIZED as #define or enum - found
-- Looking for MPI_COMBINER_STRUCT_INTEGER
-- Looking for MPI_COMBINER_STRUCT_INTEGER - not found
-- Looking for MPI_COMBINER_STRUCT_INTEGER as #define or enum
-- Looking for MPI_COMBINER_STRUCT_INTEGER as #define or enum - found
-- Looking for MPI_COMBINER_INDEXED_BLOCK
-- Looking for MPI_COMBINER_INDEXED_BLOCK - not found
-- Looking for MPI_COMBINER_INDEXED_BLOCK as #define or enum
-- Looking for MPI_COMBINER_INDEXED_BLOCK as #define or enum - found
-- Looking for MPI_COMBINER_F90_REAL
-- Looking for MPI_COMBINER_F90_REAL - not found
-- Looking for MPI_COMBINER_F90_REAL as #define or enum
-- Looking for MPI_COMBINER_F90_REAL as #define or enum - found
-- Looking for MPI_COMBINER_F90_INTEGER
-- Looking for MPI_COMBINER_F90_INTEGER - not found
-- Looking for MPI_COMBINER_F90_INTEGER as #define or enum
-- Looking for MPI_COMBINER_F90_INTEGER as #define or enum - found
-- Looking for MPI_COMBINER_F90_COMPLEX
-- Looking for MPI_COMBINER_F90_COMPLEX - not found
-- Looking for MPI_COMBINER_F90_COMPLEX as #define or enum
-- Looking for MPI_COMBINER_F90_COMPLEX as #define or enum - found
-- Looking for MPI_CHARACTER
-- Looking for MPI_CHARACTER - found
-- Looking for MPI_REAL
-- Looking for MPI_REAL - found
-- Looking for MPI_INTEGER
-- Looking for MPI_INTEGER - found
-- Looking for MPI_DOUBLE_PRECISION
-- Looking for MPI_DOUBLE_PRECISION - found
-- Looking for MPI_INTEGER1
-- Looking for MPI_INTEGER1 - found
-- Looking for MPI_INTEGER2
-- Looking for MPI_INTEGER2 - found
-- Looking for MPI_INTEGER4
-- Looking for MPI_INTEGER4 - found
-- Looking for MPI_INTEGER8
-- Looking for MPI_INTEGER8 - found
-- Looking for MPI_INTEGER16
-- Looking for MPI_INTEGER16 - found
-- Looking for MPI_REAL4
-- Looking for MPI_REAL4 - found
-- Looking for MPI_REAL8
-- Looking for MPI_REAL8 - found
-- Looking for MPI_REAL16
-- Looking for MPI_REAL16 - found
-- Looking for MPI_COMPLEX8
-- Looking for MPI_COMPLEX8 - found
-- Looking for MPI_COMPLEX16
-- Looking for MPI_COMPLEX16 - found
-- Looking for MPI_COMPLEX32
-- Looking for MPI_COMPLEX32 - found
-- Looking for MPI_UB
-- Looking for MPI_UB - found
-- Looking for MPI_LB
-- Looking for MPI_LB - found
-- Looking for strerror
-- Looking for strerror - found
-- Looking for MPI_Request_get_status
-- Looking for MPI_Request_get_status - found
-- Looking for MPI_Type_dup
-- Looking for MPI_Type_dup - found
-- Looking for MPI_Info_dup
-- Looking for MPI_Info_dup - found
-- Check size of ssize_t
-- Check size of ssize_t - done
-- Check size of uchar
-- Check size of uchar - failed
-- Check size of MPI_Offset
-- Check size of MPI_Offset - failed
-- Check size of ((struct stat*)0)->st_blksize
-- Check size of ((struct stat*)0)->st_blksize - failed
-- Looking for mpio.h
-- Looking for mpio.h - found
-- Reticulating splines...
If you can't see the following build report, then you need to turn off COLOR_CMAKE_MESSAGES
-- **************************************************************************
--                               Build Report
--                              Compiler Flags:
-- C No-Opt:           -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O0
-- C Optimized:        -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native
--
-- CXX No-Opt:         -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0
-- CXX Optimized:      -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native
--
-- Fortran No-Opt:     -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O0
-- Fortran Optimized:  -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3 -mtune=native
--
--                           3rd Party Libraries
-- ---building bundled: -----------------------------------------------------
-- blas - for fundamental linear algebra calculations
-- lapack - for fundamental linear algebra calculations
-- arpack - for fundamental linear algebra calculations
-- netcdf - for creating trajectory data files
-- netcdf-fortran - for creating trajectory data files from Fortran
-- fftw - used to do Fourier transforms very quickly
-- readline - enables an interactive terminal in cpptraj
-- xblas - used for high-precision linear algebra calculations
-- boost - C++ support library
-- tng_io - enables GROMACS tng trajectory input in cpptraj
-- mpi4py - MPI support library for MMPBSA.py
-- pnetcdf - used by cpptraj for parallel trajectory output
-- ---using installed: ------------------------------------------------------
-- ucpp - used as a preprocessor for the NAB compiler
-- zlib - for various compression and decompression tasks
-- libbz2 - for bzip2 compression in cpptraj
-- libm - for fundamental math routines if they are not contained in the C library
-- perlmol - chemistry library used by FEW
-- ---disabled: ------------------------------------------------
-- c9x-complex - used as a support library on systems that do not have C99 complex.h support
-- lio - used by Sander to run certain QM routines on the GPU
-- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
-- pupil - used by Sander as an alternate user interface
-- plumed - used as an alternate MD backend for Sander
-- mkl - alternate implementation of lapack and blas that is tuned for speed
-- mbx - computes energies and forces for pmemd with the MB-pol model

--                                Features:
-- MPI:                     ON
-- OpenMP:                  OFF
-- CUDA:                    OFF
-- Build Shared Libraries:  ON
-- Build GUI Interfaces:    ON
-- Build Python Programs:   ON
--  -Python Interpreter:    Internal Miniconda (version 3.9)
-- Build Perl Programs:     ON
-- Build configuration:     RELEASE
-- Target Processor:        x86_64
-- Build Documentation:     OFF
-- Sander Variants:         normal LES API LES-API MPI LES-MPI
-- Install location:        /mnt/c/amber/amber20/
-- Installation of Tests:   ON

--                               Compilers:
--         C: GNU 9.4.0 (/usr/bin/gcc)
--       CXX: GNU 9.4.0 (/usr/bin/g++)
--   Fortran: GNU 9.4.0 (/usr/bin/gfortran)

--                              Building Tools:
-- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pymsmt pysander python_site_packages pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil

--                            NOT Building Tools:
-- quick - BUILD_QUICK is not enabled
-- reaxff_puremd - BUILD_REAXFF_PUREMD is not enabled
-- gpu_utils - Not included in AmberTools
-- pmemd - Not included in AmberTools
-- **************************************************************************
-- Environment resource files are provided to set the proper environment
-- variables to use AMBER and AmberTools. This is required to run any Python
-- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
--
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /mnt/c/amber/amber20//amber.sh file in your shell. Consider adding the line
--   test -f /mnt/c/amber/amber20//amber.sh && source /mnt/c/amber/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /mnt/c/amber/amber20//amber.csh file in your shell. Consider adding the line
--   test -f /mnt/c/amber/amber20//amber.csh && source /mnt/c/amber/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /mnt/c/amber/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/c/amber/amber20_src/build

If the cmake build report looks OK, you should now do the following:

    make install
    source /mnt/c/amber/amber20/amber.sh

Consider adding the last line to your login startup script, e.g. ~/.bashrc

mohamad@Mohamad:/mnt/c/amber/amber20_src/build$ test -f /mnt/c/amber/amber20//amber.sh && source /mnt/c/amber/amber20//amber.sh
mohamad@Mohamad:/mnt/c/amber/amber20_src/build$ make install
[  1%] Built target readline
Scanning dependencies of target fftw3_threads_obj
[  1%] Building C object AmberTools/src/fftw-3.3/threads/CMakeFiles/fftw3_threads_obj.dir/threads.c.o
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[  2%] Building C object AmberTools/src/fftw-3.3/threads/CMakeFiles/fftw3_threads_obj.dir/f77api.c.o
[  2%] Built target fftw3_threads_obj
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[  2%] Building C object AmberTools/src/fftw-3.3/api/CMakeFiles/fftw_api.dir/apiplan.c.o
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 1554 |     if (status == 0)
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[ 21%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_vars_int1f.c.o
[ 21%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_var1_int1f.c.o
[ 21%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_var_int1f.c.o
[ 21%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_vara_int1_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_vara_int1f.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_vars_int1_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_vars_int1f.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_double_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_doublef.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varmf.c.o
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[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_int2f.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_int_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_intf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_real_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_realf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_text_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_varm_textf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_double_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_doublef.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varmf.c.o
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[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_int2_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_int2f.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_int_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_intf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_real_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_realf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_text_allf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/put_varm_textf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/set_fillf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/set_default_formatf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/issyserrf.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/get_file_infof.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/deletef.c.o
[ 22%] Building Fortran object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/strerrorf.f.o
[ 22%] Building Fortran object AmberTools/src/pnetcdf/src/libf/CMakeFiles/pnetcdf_fortran_obj.dir/inq_libversf.f.o
[ 22%] Built target pnetcdf_fortran_obj
Scanning dependencies of target pnetcdf_c_obj
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/mpinetcdf.c.o
In file included from /mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/mpinetcdf.c:16:
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/mpinetcdf.c: In function ‘ncmpi_create’:
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/mpinetcdf.c:91:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   91 |   assert(ncp->xsz = ncmpii_hdr_len_NC(ncp, sizeof_off_t));
      |          ^~~
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/header.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/mpincio.c.o
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[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/dim.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/error.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/nc.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/ncx.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/string.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/var.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/pnetcdf_c_obj.dir/ncmpidtype.c.o
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/ncmpidtype.c: In function ‘ncmpii_type_filter’:
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/ncmpidtype.c:148:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  148 |         if (SIZEOF_SIZE_T == 8)
      |         ^~
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/ncmpidtype.c:150:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  150 |      if (SIZEOF_SIZE_T == 4)
      |      ^~
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/ncmpidtype.c:156:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  156 |         if (SIZEOF_SIZE_T == 8)
      |         ^~
/mnt/c/amber/amber20_src/AmberTools/src/pnetcdf/src/lib/ncmpidtype.c:158:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  158 |      if (SIZEOF_SIZE_T == 4)
      |      ^~
[ 22%] Built target pnetcdf_c_obj
Scanning dependencies of target pnetcdf
[ 22%] Linking Fortran shared library libpnetcdf.so
[ 22%] Built target pnetcdf
Scanning dependencies of target ncvalid
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/validator.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/header.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/mpincio.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/attr.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/dim.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/nc.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/ncx.c.o
[ 22%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/string.c.o
[ 23%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/error.c.o
[ 23%] Building C object AmberTools/src/pnetcdf/src/lib/CMakeFiles/ncvalid.dir/var.c.o
[ 23%] Linking C executable ncvalid
[ 23%] Built target ncvalid
Scanning dependencies of target mpi4py
[ 23%] Building mpi4py
running build
running build_src
running build_py
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/bench.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/run.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/__init__.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/__main__.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/pool.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/server.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_base.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/__init__.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/futures/__main__.py -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/futures
copying src/mpi4py/libmpi.pxd -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/MPI.pxd -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
copying src/mpi4py/__init__.pxd -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/include/mpi4py
running build_clib
MPI configuration: [cmake-mpi] from '/mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/mpi.cfg'
MPI C compiler:    /usr/bin/gcc
MPI C++ compiler:  /usr/bin/g++
checking for library 'lmpe' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -llmpe -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -llmpe
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'mpe' dylib library
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c src/lib-pmpi/mpe.c -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/mpe.o
creating /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags -Wl,--no-as-needed /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/mpe.o -L/mnt/c/amber/amber20/lib -lmpi -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -lvt-mpi -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -lvt.mpi -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c src/lib-pmpi/vt.c -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/vt.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags -Wl,--no-as-needed /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/vt.o -L/mnt/c/amber/amber20/lib -lmpi -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -lvt-mpi -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -lvt.mpi -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c src/lib-pmpi/vt-mpi.c -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-mpi.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags -Wl,--no-as-needed /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-mpi.o -L/mnt/c/amber/amber20/lib -lmpi -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -lvt-hyb -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt-hyb
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20/lib -lvt.ompi -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: cannot find -lvt.ompi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20/include -c src/lib-pmpi/vt-hyb.c -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-hyb.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags -Wl,--no-as-needed /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-hyb.o -L/mnt/c/amber/amber20/lib -lmpi -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [cmake-mpi] from '/mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/mpi.cfg'
MPI C compiler:    /usr/bin/gcc
MPI C++ compiler:  /usr/bin/g++
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9 -c _configtest.c -o _configtest.o
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -L/mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9 -c _configtest.c -o _configtest.o
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat _configtest.o -L/mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9 -c src/dynload.c -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/dynload.o
gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib -L/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/lib /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9/src/dynload.o -L/mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9 -ldl -o /mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.9/mpi4py/dl.cpython-39-x86_64-linux-gnu.so
checking for MPI compile and link ...
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9 -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include -fPIC -I/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9 -I/mnt/c/amber/amber20/include -c _configtest.c -o _configtest.o
/usr/bin/gcc -pthread -B /mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat -Wl,-rpath -Wl,/mnt/c/amber/amber20/lib -Wl,--enable-new-dtags _configtest.o -L/mnt/c/amber/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.9 -L/mnt/c/amber/amber20/lib -lmpi -o _configtest
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libm.so.6, needed by /mnt/c/amber/amber20/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libpciaccess.so.0, needed by /mnt/c/amber/amber20/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: libdl.so.2, needed by /mnt/c/amber/amber20/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: warning: librt.so.1, needed by /mnt/c/amber/amber20/lib/libmpi.so, not found (try using -rpath or -rpath-link)
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `aio_return@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `aio_read@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `aio_suspend@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `dlopen@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `dlerror@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_iterator_destroy'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_device_cfg_read'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `dlclose@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_device_probe'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `shm_open@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_system_cleanup'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_device_next'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `dlsym@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_slot_match_iterator_create'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_get_strings'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `pci_system_init'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `shm_unlink@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `aio_error@GLIBC_2.2.5'
/mnt/c/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat/ld: /mnt/c/amber/amber20/lib/libmpi.so: undefined reference to `aio_write@GLIBC_2.2.5'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!
make[2]: *** [AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py.dir/build.make:276: AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp] Error 1
make[1]: *** [CMakeFiles/Makefile2:4783: AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py.dir/all] Error 2
make: *** [Makefile:152: all] Error 2