If gnu doesn’t work try clang.
On Wed, Mar 30, 2022 at 4:54 PM Daniel Roe <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%7C722a6744098740f71aaa08da12836e74%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842652940616131%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rS0A3wHi%2Fxd%2FvEJeXhDC6krW2sKG7Pao%2Bw%2B7Wjdvqto%3D&reserved=0
>> >
>> > -Dan
>> >
>> > On Wed, Mar 16, 2022 at 9:45 AM Matthew Guberman-Pfeffer
>> > <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
>> >>
>> >>
>> >>
>> >>
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>> >
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Received on Wed Mar 30 2022 - 14:00:03 PDT
