Hi Gustaf and Dan
Actually I already installed the zlib1g-dev and libbz2-dev using the sudo apt-get command. When I did sudo apt search, these two packages appeared. I also installed xorg-dev. Anyway,
I tried to examine why leap was having an error. When I separately performed make install on the leap folder, this is what I found:
//redacted; all programs prior to xaleap were okay
[LEAP] CC xaLeap
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../Xraw/libXaw.a(AsciiSrc.o): in function `InitStringOrFile':
AsciiSrc.c:(.text.InitStringOrFile+0x1a8): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libuuid.so.1, needed by /usr/lib/x86_64-linux-gnu/libSM.so, not found (try using -rpath or -rpath-link)
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libbsd.so.0, needed by /usr/lib/x86_64-linux-gnu/libICE.so, not found (try using -rpath or -rpath-link)
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libxcb.so.1, needed by /usr/lib/x86_64-linux-gnu/libX11.so, not found (try using -rpath or -rpath-link)
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_connection_has_error'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_get_maximum_request_length'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libSM.so: undefined reference to `uuid_unparse_lower.UUID_1.0'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_wait_for_reply64'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_get_file_descriptor'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_connect'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libICE.so: undefined reference to `arc4random_buf.LIBBSD_0.2'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_get_setup'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_wait_for_event'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_poll_for_event'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_parse_display'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_generate_id'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libSM.so: undefined reference to `uuid_generate.UUID_1.0'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_disconnect'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_take_socket'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_poll_for_reply64'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_writev'
/home/itsrdc/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libX11.so: undefined reference to `xcb_connect_to_display_with_auth_info'
collect2: error: ld returned 1 exit status
When I checked the config.h, it automatically referred to the Anaconda3 folder when I miniconda was supposed to compile for Amber 18. My hypothesis is it was supposed to be x86_64-conda_cos6-linux gnu that should be called when configuring the gnu of Amber (I installed Anaconda separately because I have another program that requires conda outside of Amber 18). So I needed to delete both Amber 18 and Anaconda 3 including all programs I was using since I do not know how to edit the config.h. I reinstalled Amber 18 first and during ./configure gnu this already appeared:
Checking for zlib: OK
Checking for libbz2: OK
Then I checked the config.h and unlike the previous one, the cc already referred to gcc and not Anaconda3 folder. And now it is already working. Thanks for the help!
Joanna
________________________________
From: Gustaf Olsson <gustaf.olsson.lnu.se>
Sent: Friday, June 26, 2020 3:58 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Problems with Make install Amber 18
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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Jun 26 2020 - 04:30:04 PDT
