Using clang gives:
fftw3 enabled.
C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
Fortran compiler (FC) set to /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
Testing C++ compiler: OK
Testing C compiler: OK
Testing Fortran compiler: OK
Testing basic C++11 support: OK
Testing system headers for C++11 support: OK
Testing clang C++/Fortran linking: dyld: Library not loaded: @rpath/libgfortran.5.dylib
Referenced from: /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/./testp
Reason: image not found
./configure: line 479: 20271 Abort trap: 6 ./testp > prog.out
Error: Run of test program failed, compiled with: x86_64-apple-darwin13.4.0-clang++ -o testp testc.o testf.o -L/opt/anaconda3/envs/AmberTools20/lib/gcc/x86_64-apple-darwin13.4.0/9.3.0/../../../ -lgfortran -L/usr/local/opt/lapack/lib
> On Mar 30, 2022, at 4:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> If gnu doesn’t work try clang.
>
> On Wed, Mar 30, 2022 at 4:54 PM Daniel Roe <daniel.r.roe.gmail.com <mailto:daniel.r.roe.gmail.com>> wrote:
>
>> Hi,
>>
>> Try configure -fftw3 —buildlibs gnu
>>
>> -Dan
>>
>> On Wed, Mar 30, 2022 at 4:40 PM Matthew Guberman-Pfeffer <
>> matthew.guberman-pfeffer.uconn.edu> wrote:
>>
>>> Hi Dan,
>>>
>>> Thanks! I tried to install cpptraj from GitHub on my Mac, but had the
>>> below errors:
>>>
>>> I tried ./configure gnu -amberlib and got the below error:
>>>
>>> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
>>> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
>>> Fortran compiler (FC) set to
>>> /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
>>>
>>> Testing C++ compiler: OK
>>> Testing C compiler: OK
>>> Testing Fortran compiler: OK
>>> Testing basic C++11 support: OK
>>> Testing system headers for C++11 support: OK
>>> Using blas from /opt/anaconda3/envs/AmberTools20
>>> Using lapack from /opt/anaconda3/envs/AmberTools20
>>> Using netcdf from /opt/anaconda3/envs/AmberTools20
>>> Warning: Cannot link 'lapack' statically.
>>> Warning: Cannot link 'blas' statically.
>>> Checking BZLIB: OK
>>> Checking ZLIB: OK
>>> Checking NetCDF: Failed.
>>> Error: NetCDF build/link failed:
>>> x86_64-apple-darwin13.4.0-clang++ -Wall -O3 -march=core2
>>> -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
>>> -fstack-protector-strong -O2 -pipe -stdlib=libc++
>>> -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem
>>> /opt/anaconda3/envs/AmberTools20/include -std=gnu++11 -
>>> I/opt/anaconda3/envs/AmberTools20/include -o testp testp.cpp
>>> /opt/anaconda3/envs/AmberTools20/lib/libnetcdf.a
>>> -L/usr/local/opt/lapack/lib
>>> Error: Error message follows:
>>> Error: Undefined symbols for architecture x86_64:
>>>
>>> I tried ./configure gnu and got the below error:
>>>
>>> C++ compiler (CXX) set to x86_64-apple-darwin13.4.0-clang++
>>> C compiler (CC) set to x86_64-apple-darwin13.4.0-clang
>>> Fortran compiler (FC) set to
>>> /opt/anaconda3/envs/AmberTools20/bin/x86_64-apple-darwin13.4.0-gfortran
>>>
>>> Testing C++ compiler: OK
>>> Testing C compiler: OK
>>> Testing Fortran compiler: OK
>>> Testing basic C++11 support: OK
>>> Testing system headers for C++11 support: OK
>>> Checking BZLIB: OK
>>> Checking ZLIB: OK
>>> Checking NetCDF: Checking for bundled NetCDF: OK
>>> Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: Should
>>> CPPTRAJ attempt to build its own lapack? {y|n}: y
>>> Configuring lapack... (using generated make.inc) Success.
>>> ./get_library.sh: line 183: nproc: command not found
>>> MAKE_COMMAND is not set; set to 'make -j6'
>>> Compiling lapack (may be time-consuming)... Build failed.
>>> Check
>>> /Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/lapack_compile.log
>>> for errors.
>>> Error: Building LAPACK/BLAS failed.
>>>
>>> Best,
>>> Matthew
>>>
>>>
>>>
>>>> On Mar 30, 2022, at 3:27 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>
>>>> *Message sent from a system outside of UConn.*
>>>>
>>>>
>>>> Hi,
>>>>
>>>> I recently added this feature to GitHub cpptraj (version 6.4.5). Let
>>>> me know if it works for you if you get a chance to try it. More
>>>> details here:
>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAmber-MD%2Fcpptraj%2Fpull%2F960&data=04%7C01%7C%7C7c9a084792fe4296d8e708da128f9727%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705170711077%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=MnCsOnamCgy9NhF2asoqz4KXVjQTJ0IepWm0Owd%2B7Mg%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAmber-MD%2Fcpptraj%2Fpull%2F960&data=04%7C01%7C%7C7c9a084792fe4296d8e708da128f9727%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705170711077%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=MnCsOnamCgy9NhF2asoqz4KXVjQTJ0IepWm0Owd%2B7Mg%3D&reserved=0>
>>>>
>>>> -Dan
>>>>
>>>> On Wed, Mar 16, 2022 at 9:45 AM Matthew Guberman-Pfeffer
>>>> <matthew.guberman-pfeffer.uconn.edu <mailto:matthew.guberman-pfeffer.uconn.edu>> wrote:
>>>>>
>>>>> Dear Amber Community,
>>>>>
>>>>> I need to quantify the total number of H-bonds for each pair of
>>> residues in my protein. That would mean a 1321 x 1321 matrix. I am having
>>> trouble in writing a bash script to process the CPPTRAJ hbond output (e.g.
>>> All.UU.avg.dat) to compute each matrix element. I’ve thought of running
>>> CPPTRAJ for every possible pair of donormask and acceptormask, but this is
>>> truly an ugly brute-force approach. Does anyone have suggestions on how I
>>> can compute the total number of H-bonds between each pair of residues?
>>>>>
>>>>> Best,
>>>>> Matthew
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>>>>
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>>>>
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>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C7c9a084792fe4296d8e708da128f9727%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705170711077%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0W4oDsKngmcMAQk%2B1ZYFXlUszht3NgP5Jz3AL2vujYw%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7C7c9a084792fe4296d8e708da128f9727%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842705170711077%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0W4oDsKngmcMAQk%2B1ZYFXlUszht3NgP5Jz3AL2vujYw%3D&reserved=0>
>>>
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>>>
>>
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Received on Wed Mar 30 2022 - 14:30:02 PDT
