Checking for updates... Checking for available patches online. This may take a few seconds... Available AmberTools 14 patches: update.24 (modifies pbsa, sander) Released on Jan 5 2015 (written by Ray Luo) Description: reset igb flag in addition to ipb so pbsa cannot be turned on in sander when no charge or radius is read in. update.25 (modifies cpptraj) Released on January 23, 2015 (written by Daniel R. Roe) Description: Fixes for cpptraj: update to version 14.25 1) Fix autoimage centering to box center for general triclinic cells. 2) Make selection of reference structure by name/tag more robust. 3) Fix bug where reference structure was always being centered in 2drms 'nofit' calc. 4) Fix OpenMP-related segfaults with TRAJ data sets and in the checkstructure action. update.26 (modifies sander) Released on January 29, 2015 (written by Ray Luo) Description: Fixes test case sander_pbsa_decres Available Amber 14 patches: update.11 (modifies pmemd.cuda) Released on 09 February 2015 (written by Perri Needham, Ross Walker, Scott Le Grand) Description: Bugfixes effecting emap, restraints and the GB implementation. emap: A check has been added to prevent emap restraints as they are not yet supported on the GPU. COM restraints: The number of atoms in a COM grouping has been increased from 200 to 1024. A bug has been fixed that was preventing distance restraints from correctly being detected when the restrain involved atom 1. GB: Fixes undocumented uninitialized variable in DPFP GB simulations that was causing inconsistent results. There are patches available. Do you want to apply them now? [y/N] (Recommended Y) Preparing to apply updates... please wait. Downloading updates for AmberTools 14 Downloading AmberTools 14/update.24 (1.59 KB) Applying AmberTools 14/update.24 Downloading AmberTools 14/update.25 (8.85 KB) Applying AmberTools 14/update.25 Downloading AmberTools 14/update.26 (2.17 KB) Applying AmberTools 14/update.26 Downloading updates for Amber 14 Downloading Amber 14/update.11 (6.88 KB) Applying Amber 14/update.11 NOTE: update_amber only updates the raw source code! You must recompile if you want any changes to take effect! Searching for python2... Found python2.6: /usr/bin/python2.6 Obtaining the gnu suite version: gcc -v The version is 4.4.7 Testing the gcc compiler: gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c OK Testing the g++ compiler: g++ -o testp testp.cpp OK Testing the gfortran compiler: gfortran -O0 -o testp testp.f OK Testing mixed C/Fortran compilation: gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c gfortran -O0 -c -o testp.f.o testp.f gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w OK Testing pointer size: gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c Detected 64 bit operating system. Testing flex: OK Checking NetCDF... Using bundled NetCDF library. Using existing NetCDF in '/private/gnss/amber14' Checking for zlib: OK Checking for libbz2: OK Configuring fftw-3.3 for mdgx (may be time-consuming)... fftw-3.3 configure succeeded. testing [C++ / fortran] cross-compile with MPI libsError! Unable to compile F90 code with the command: mpif90 -c testF90_main.F90 Configure failed due to the errors above!