Are there any errors in
/Users/matthewguberman-pfeffer/PersonalDIR/Desktop/Programs/cpptraj/lapack_compile.log
?
On Wed, Mar 30, 2022 at 7:12 PM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> I downloaded from that link now. If I try with clang, I get:
>
> 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: 23112 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
>
> If I try with GNU, I get:
> (AmberTools20) cpptraj >> ./configure -fftw3 --buildlibs gnu
> 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
> Enabled libraries will be built if not present.
> Checking BZLIB: OK
> Checking ZLIB: OK
> Checking NetCDF: Checking for bundled NetCDF: Downloading netcdf...
> --2022-03-30 19:10:26-- ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz
> => ‘netcdf-4.6.1.tar.gz’
> Resolving ftp.unidata.ucar.edu (ftp.unidata.ucar.edu)... 128.117.149.10
> Connecting to ftp.unidata.ucar.edu (ftp.unidata.ucar.edu)|128.117.149.10|:21... connected.
> Logging in as anonymous ... Logged in!
> ==> SYST ... done. ==> PWD ... done.
> ==> TYPE I ... done. ==> CWD (1) /pub/netcdf ... done.
> ==> SIZE netcdf-4.6.1.tar.gz ... 5693557
> ==> PASV ... done. ==> RETR netcdf-4.6.1.tar.gz ... done.
> Length: 5693557 (5.4M) (unauthoritative)
>
> netcdf-4.6.1.tar.gz 100%[=====================================================================================================================>] 5.43M 2.25MB/s in 2.4s
>
> 2022-03-30 19:10:29 (2.25 MB/s) - ‘netcdf-4.6.1.tar.gz’ saved [5693557]
>
> Unpacking netcdf...
> Configuring netcdf... Success.
> ./get_library.sh: line 183: nproc: command not found
> MAKE_COMMAND is not set; set to 'make -j6'
> Compiling netcdf (may be time-consuming)... Success.
> Checking built NetCDF: OK
> Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: Downloading lapack...
> --2022-03-30 19:11:02-- https://github.com/Reference-LAPACK/lapack/archive/v3.9.0.tar.gz
> Resolving github.com (github.com)... 140.82.113.4
> Connecting to github.com (github.com)|140.82.113.4|:443... connected.
> HTTP request sent, awaiting response... 302 Found
> Location: https://codeload.github.com/Reference-LAPACK/lapack/tar.gz/refs/tags/v3.9.0 [following]
> --2022-03-30 19:11:02-- https://codeload.github.com/Reference-LAPACK/lapack/tar.gz/refs/tags/v3.9.0
> Resolving codeload.github.com (codeload.github.com)... 140.82.114.9
> Connecting to codeload.github.com (codeload.github.com)|140.82.114.9|:443... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: unspecified [application/x-gzip]
> Saving to: ‘v3.9.0.tar.gz’
>
> v3.9.0.tar.gz [ <=> ] 7.18M 5.04MB/s in 1.4s
>
> 2022-03-30 19:11:04 (5.04 MB/s) - ‘v3.9.0.tar.gz’ saved [7534567]
>
> Unpacking lapack...
> 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 7:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > *Message sent from a system outside of UConn.*
> >
> >
> > Hi,
> >
> > On Wed, Mar 30, 2022 at 4:59 PM Matthew Guberman-Pfeffer
> > <matthew.guberman-pfeffer.uconn.edu> wrote:
> >> Error: Unrecognized Option '—buildlibs'. Use '-h' or '--help' for help.
> >
> > This indicates you're using an older version. Make sure you're using
> > the GitHub version (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAmber-MD%2Fcpptraj&data=04%7C01%7C%7Cbb0dd77f17d447c200ad08da12a1dbf7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842783647669025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=AZPqAHW7xNt2OpAdSesgIX3lvTnkdkNFTTamlM5YVpY%3D&reserved=0); this is the
> > only version with the new hbond matrix functionality.
> >
> > Once you've got the GitHub version, try
> >
> > ./configure -fftw3 --buildlibs clang
> >
> > Since it seems like you have clang and not GNU compilers.
> >
> > -Dan
> >
> >>
> >> Then, I tried:
> >> (AmberTools20) cpptraj >> ./configure -fftw3 gnu
> >> 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
> >> 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 4:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>>
> >>> *Message sent from a system outside of UConn.*
> >>>
> >>>
> >>> 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%7Cbb0dd77f17d447c200ad08da12a1dbf7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842783647669025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=QhUPrwlelvtKlQBOH0TDpnqBQr0b7MZhjMrND0Ntjck%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
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>>
> >>>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7C%7Cbb0dd77f17d447c200ad08da12a1dbf7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637842783647669025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=oFNG%2BMeadjjlIp5wVMQ7NFj%2FWhM75r4lzwquSH%2FLyNs%3D&reserved=0
> >>>>>
> >>>>> _______________________________________________
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> >>>>
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> >>
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> >
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Received on Wed Mar 30 2022 - 17:00:02 PDT
