Hi,
In addition to what Gustaf said, your compile is failing on xleap, so make
sure you have the X11 libraries installed (‘apt-get install xorg-dev’) or
disable X11 stuff by configuring with ‘-noX11’).
-Dan
On Fri, Jun 26, 2020 at 3:58 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> I have not installed the prerequisites not installed by miniconda using
> conda, as these are assumed to be present on the system before running the
> ./configure script.
>
> This might not solve the entire problem though the packages you are
> looking for are zlib1g-dev libbz2-dev. It is possible you can install these
> using ‘conda install’ though if this does not work or solve the problem,
> these must be installed and exist outside of the conda ecosystem and you
> should use:
>
> sudo apt-get install zlib1g-dev libbz2-dev
>
> Before doing the ./configure.
>
> Just a first suggestion to get past the configuration without errors.
>
> Best regards
> // Gustaf
>
>
> > On 26 Jun 2020, at 09:25, Joanna Michelle E. Chua <
> jmechua.pnri.dost.gov.ph> wrote:
> >
> > Hi Gustaf,
> >
> > This is the following output when I did ./configure gnu:
> >
> > Checking for updates...
> > Checking for available patches online. This may take a few seconds...
> >
> > Available AmberTools 19 patches:
> >
> > No patches available
> >
> > Available Amber 18 patches:
> >
> > No patches available
> >
> >
> > AMBER_PREFIX=/home/itsrdc/amber18
> > AMBER_SOURCE=/home/itsrdc/amber18
> >
> > Using the AmberTools miniconda installation in
> /home/itsrdc/amber18/miniconda
> > version 2.7.16
> >
> > Obtaining the gnu compiler suite versions, e.g.:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -v
> > The C version is 7.3.0
> > The Fortran version is 7.5.0
> >
> > Testing the /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc
> compiler:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -fPIC
> -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/itsrdc/anaconda3/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -o testp testp.c
> > OK
> >
> > Testing the /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++
> compiler:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -fPIC
> -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona
> -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
> -ffunction-sections -pipe -isystem /home/itsrdc/anaconda3/include -o testp
> testp.cpp
> > OK
> >
> > Testing the gfortran compiler:
> > gfortran -fPIC -O0 -o testp testp.f
> > OK
> >
> > Testing mixed C/Fortran compilation:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -fPIC
> -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/itsrdc/anaconda3/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -c -o testp.c.o testp.c
> > gfortran -fPIC -O0 -c -o testp.f.o testp.f
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -fPIC
> -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/itsrdc/anaconda3/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -o testp testp.c.o testp.f.o -lgfortran -w
> > OK
> >
> > Testing pointer size:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -fPIC
> -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/itsrdc/anaconda3/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -o test_pointer_size test_pointer_size.c
> > Detected 64 bit operating system.
> >
> > Testing flex:OK
> >
> > Testing bison:
> > OK
> >
> > Checking NetCDF...
> > Using bundled NetCDF library.
> > Using existing NetCDF in '/home/itsrdc/amber18'
> >
> > Checking for zlib:
> > Warning: Could not link to zlib. Ensure zlib libraries/headers are
> installed.
> > Warning: Failed command:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -fPIC
> -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/itsrdc/anaconda3/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -lz -o testp testp.c
> > Warning: Check zlib.compile.err for error details.
> > Warning: Gzip compression/decompression not available.
> >
> > Checking for libbz2:
> > Warning: Could not link to libbz2. Ensure libbz2 libraries/headers are
> installed.
> > Warning: Failed command:
> > /home/itsrdc/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -fPIC
> -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/itsrdc/anaconda3/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -lbz2 -o testp testp.c
> > Warning: Check bzlib.compile.err for error details.
> > Warning: Bzip2 compression/decompression not available.
> >
> > Configuring fftw-3.3 (may be time-consuming)...
> >
> > fftw-3.3 configure succeeded.
> >
> > Configuring boost (may be time-consuming)...OK
> > Compiling boost (may be time-consuming)...OK
> >
> > Configuring XBLAS (may be time-consuming)...
> >
> > XBLAS configure succeeded.
> >
> > Configuring CPPTRAJ...complete.
> >
> > The configuration file, config.h, was successfully created.
> >
> >
> --------------------------------------------------------------------------------
> > Environment resource files are provided to set the proper environment
> > variables to use AMBER and AmberTools. This is required to run any Python
> > programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
> >
> > If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> > /home/itsrdc/amber18/amber.sh file in your shell. Consider adding the
> line
> > test -f /home/itsrdc/amber18/amber.sh && source
> /home/itsrdc/amber18/amber.sh
> > to your startup file (e.g., ~/.bashrc)
> >
> > If you use a C shell (e.g., csh, tcsh), source the
> > /home/itsrdc/amber18/amber.csh file in your shell. Consider adding the
> line
> > test -f /home/itsrdc/amber18/amber.csh && source
> /home/itsrdc/amber18/amber.csh
> > to your startup file (e.g., ~/.cshrc)
> >
> > NOTE: MacOS users might need to add the content to ~/.bash_profile file
> > (You need to do the above before running 'make install')
> >
> --------------------------------------------------------------------------------
> >
> > The next step is to source the amber.sh or amber.csh file
> > (if needed, see above), and then to type 'make install'
> >
> > Cleaning the src directories. This may take a few moments.
> > Configure complete.
> >
> >
> > Since I saw that both the zlib an bzip2 had an error (highlighted in
> yellow), I tried the following:
> >
> > (base) itsrdc.itsrdc:~/amber18$ conda install zlib
> > Collecting package metadata (current_repodata.json): done
> > Solving environment: done
> >
> > # All requested packages already installed.
> >
> > (base) itsrdc.itsrdc:~/amber18$ conda install bzip2
> > Collecting package metadata (current_repodata.json): done
> > Solving environment: done
> >
> > # All requested packages already installed.
> >
> > When I did ./configure gnu again, the same error still occurred but I
> then proceeded with source then make install and the same problem still
> appeared.
> >
> > Makefile:192: recipe for target 'xaLeap' failed
> > make[4]: *** [xaLeap] Error 1
> > make[4]: Leaving directory
> '/home/itsrdc/amber18/AmberTools/src/leap/src/leap'
> > Makefile:18: recipe for target 'install_xleap' failed
> > make[3]: *** [install_xleap] Error 2
> > make[3]: Leaving directory '/home/itsrdc/amber18/AmberTools/src/leap'
> > Makefile:4: recipe for target 'install' failed
> > make[2]: *** [install] Error 2
> > make[2]: Leaving directory '/home/itsrdc/amber18/AmberTools/src/leap'
> > Makefile:26: recipe for target 'serial' failed
> > make[1]: *** [serial] Error 2
> > make[1]: Leaving directory '/home/itsrdc/amber18/AmberTools/src'
> > Makefile:7: recipe for target 'install' failed
> > make: *** [install] Error 2
> >
> > Joanna
> >
> >
> > ________________________________
> > From: Gustaf Olsson <gustaf.olsson.lnu.se>
> > Sent: Friday, June 26, 2020 2:03 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Problems with Make install Amber 18
> >
> > Assuming all of the other prerequisites are covered regarding compilers
> and things, having untarred the tarball you should
> >
> > $ cd /path/to/amber18
> >
> > and running pwd should produce something ending in /amber18, as in
> >
> > /home/xxxxxxx/amber18
> >
> > Assuming your username is xxxxxxx and you unpacked the tarball in you
> user home directory. Once this is done you should start by running:
> >
> > ./configure gnu
> >
> > You should then allow updates to install, do use miniconda to install
> other dependencies to make life easier and finally, depending on the output
> from the configure script, once it stops running, you should either compile
> using “make install” or post any additional errors here.
> >
> > Fingers crossed and best regards
> > // Gustaf
> >
> >
> >> On 26 Jun 2020, at 01:38, Joanna Michelle E. Chua <
> jmechua.pnri.dost.gov.ph> wrote:
> >>
> >> Hi Renato
> >>
> >> I mixed up sorry. I did config gnu. Should I paste the entire result?
> >>
> >> Joanna
> >>
> >> Get Outlook for Android<https://aka.ms/ghei36>
> >> ________________________________
> >> From: Renato Araujo <renatoacufpa.gmail.com>
> >> Sent: Friday, June 26, 2020 1:32:54 AM
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] Problems with Make install Amber 18
> >>
> >> Hi Joanna
> >>
> >> You gave the command
> >>
> >> . \ configure gnu
> >>
> >> in the amber18 directory.
> >>
> >> Then he exulted
> >>
> >> make install
> >>
> >> Is that what you did?
> >>
> >> Renato
> >>
> >> Em qui., 25 de jun. de 2020 às 13:08, Joanna Michelle E. Chua <
> >> jmechua.pnri.dost.gov.ph> escreveu:
> >>
> >>> Hi Gustaf,
> >>>
> >>> I am installing Amber 18 using Ubuntu 18.04 LTS.
> >>>
> >>> When I perform ./configure /home/user/amber18 there is no output. And
> yes
> >>> I already added AMBERHOME in my path.
> >>>
> >>> Joanna
> >>> ________________________________
> >>> From: Gustaf Olsson <gustaf.olsson.lnu.se>
> >>> Sent: Thursday, June 25, 2020 2:15 PM
> >>> To: AMBER Mailing List <amber.ambermd.org>
> >>> Subject: Re: [AMBER] Problems with Make install Amber 18
> >>>
> >>> Well, with a lot of unknowns it is hard to say.
> >>>
> >>> On what OS and version are you trying to compile?
> >>>
> >>> What settings did you use running the “./configure” script and what was
> >>> the output?
> >>>
> >>> Have you added AMBERHOME to you path?
> >>>
> >>> With this information it might be a little bit easier to provide
> >>> suggestions on how to proceed.
> >>>
> >>> Best regards
> >>> // Gustaf
> >>>
> >>>
> >>>> On 25 Jun 2020, at 05:26, Joanna Michelle E. Chua <
> >>> jmechua.pnri.dost.gov.ph> wrote:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> Whenever I perform make install I see these failed codes
> >>>>
> >>>> Makefile:192: recipe for target 'xaLeap' failed
> >>>> make[4]: *** [xaLeap] Error 1
> >>>> make[4]: Leaving directory
> >>> '/home/itsrdc/amber18/AmberTools/src/leap/src/leap'
> >>>> Makefile:18: recipe for target 'install_xleap' failed
> >>>> make[3]: *** [install_xleap] Error 2
> >>>> make[3]: Leaving directory '/home/itsrdc/amber18/AmberTools/src/leap'
> >>>> Makefile:4: recipe for target 'install' failed
> >>>> make[2]: *** [install] Error 2
> >>>> make[2]: Leaving directory '/home/itsrdc/amber18/AmberTools/src/leap'
> >>>> Makefile:26: recipe for target 'serial' failed
> >>>> make[1]: *** [serial] Error 2
> >>>> make[1]: Leaving directory '/home/itsrdc/amber18/AmberTools/src'
> >>>> Makefile:7: recipe for target 'install' failed
> >>>> make: *** [install] Error 2
> >>>>
> >>>> It was consistent. whenever I perform make clean and repeat the source
> >>> and make install again I still see the same. Has anyone experienced the
> >>> same? Thank you.
> >>>>
> >>>> Joanna Michelle Chua, RPh
> >>>> Science Research Specialist I
> >>>> Isotope Techniques Section
> >>>> Nuclear Services Division
> >>>> Philippine Nuclear Research Institute
> >>>> Tel. no. (+632) 8929 6011 to 14 loc. 240
> >>>> Mobile No. (+63) 917 845 4137
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >> --
> >> Prof Dr Renato Costa
> >> Instituto Federal do Pará - IFPA
> >> Grupo de Modelagem Molecular - UFPA
> >> Tel.+55 91 985484622
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>
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Received on Fri Jun 26 2020 - 03:30:03 PDT
