[AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler

From: Samuel Mohan Dass, Premila <premila.illinois.edu>
Date: Mon, 8 Mar 2021 19:20:52 +0000

Hi I was trying the Cmake installation and got the following error after typing make_install, could use help:

ifort: error #10105: /jet/packages/intel/compilers_and_libraries_2020.4.304/linux/bin/intel64/fortcom: core dumped
ifort: warning #10102: unknown signal(21370896)
ifort: error #10106: Fatal error in /jet/packages/intel/compilers_and_libraries_2020.4.304/linux/bin/intel64/fortcom, terminated by unknown
compilation aborted for /ocean/projects/mcb200041p/premila/amber20_src/AmberTools/src/sander/ips.F90 (code 1)
make[2]: *** [AmberTools/src/sander/CMakeFiles/sander_base_obj.dir/build.make:271: AmberTools/src/sander/CMakeFiles/sander_base_obj.dir/ips.F90.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:2528: AmberTools/src/sander/CMakeFiles/sander_base_obj.dir/all] Error 2
make: *** [Makefile:152: all] Error 2

The only edit I did in the cmake_script:



My build report is as following for the make_script:
                            Build Report
-- Compiler Flags:
-- C No-Opt: -O0
-- C Optimized: -ip -O3 -xHost

-- 
-- CXX No-Opt:        -O0 
-- CXX Optimized:     -O3 
-- 
-- Fortran No-Opt:     -warn all -warn nounused -warn nointerfaces -O0 
-- Fortran Optimized:  -warn all -warn nounused -warn nointerfaces -ip -O3 -xHost 
-- 
--                           3rd Party Libraries 
-- ---building bundled: ----------------------------------------------------- 
-- arpack - for fundamental linear algebra calculations 
-- ucpp - used as a preprocessor for the NAB compiler 
-- netcdf - for creating trajectory data files 
-- netcdf-fortran - for creating trajectory data files from Fortran 
-- xblas - used for high-precision linear algebra calculations 
-- boost - C++ support library 
-- perlmol - chemistry library used by FEW 
-- ---using installed: ------------------------------------------------------ 
-- blas - for fundamental linear algebra calculations 
-- lapack - for fundamental linear algebra calculations 
-- fftw - used to do Fourier transforms very quickly 
-- readline - used for the console functionality of cpptraj 
-- 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 
-- ---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:                     OFF 
-- OpenMP:                  OFF 
-- CUDA:                    OFF 
-- Build Shared Libraries:  ON 
-- Build GUI Interfaces:    ON 
-- Build Python Programs:   ON 
--  -Python Interpreter:    Internal Miniconda (version 3.8) 
-- Build Perl Programs:     ON 
-- Build configuration:     RELEASE 
-- Target Processor:        x86_64 
-- Build Documentation:     OFF 
-- Sander Variants:         normal LES API LES-API 
-- Install location:        /ocean/projects/mcb200041p/premila/amber20/ 
-- Installation of Tests:   ON 
--                               Compilers: 
--         C: Intel 19.1.3.20200925 (/opt/intel/compilers_and_libraries_2020.4.304/linux/bin/intel64/icc) 
--       CXX: Intel 19.1.3.20200925 (/opt/intel/compilers_and_libraries_2020.4.304/linux/bin/intel64/icpc) 
--   Fortran: Intel 19.1.3.20200925 (/opt/intel/compilers_and_libraries_2020.4.304/linux/bin/intel64/ifort) 
--                              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 pmemd pymsmt pysander pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil 
--                            NOT Building Tools: 
-- quick - In-development programs are disabled. 
-- pymdgx - In-development programs are disabled. 
-- gpu_utils - Requires CUDA
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Received on Mon Mar 08 2021 - 11:30:02 PST