2DX Installation

2DX v2

• Nov 14 2007
• installed version 2.1
• rpm does not work on any of our linux boxes -- gives floating point exception
• needed to recompile from scratch, did so on CentOS4^? laptop, then put in /cryoem

Installed fftw3

• download fftw-3.1.2.tar.gz and untar in /usr/local/src
• install as follows:

    ./configure --enable-float
    make
    make install
  

• libraries are in /usr/local/lib

Install QT 4.3

• download qt-x11-opensource-src-4.3.2.tar.gz
• untar into /usr/local/src
• install as follows:

   ./configure
  qmake
  qmake install
  

• takes a very long time
• QT4.3 will be in /usr/local/Trolltech

Install CCP4

• download tarfile
• install in /cryoem/CCP4

Compile 2dx

• downloaded 2dx-2.1.0.tar.bz2 and uncompressed
• set up libstdc++ library location:

  ln -s /usr/lib/gcc/i386-redhat-linux/3.4.3/libstdc++.a /usr/lib/.
  

• compile:

  ./configure
  make
  

• At this point, several programs will refuse to compile because of problems with flags.
• need to edit the following files:
  • ./mrc/source/2dx_getlat/Makefile
  • ./mrc/source/Makefile
  • ./mrc/source/endianness/Makefile
  • ./mrc/source/peaksearch/Makefile
• Delete any flags that say -ftree-vectorize
• now, continue compiling:

  make
  make install
  

• 2dx will be in /usr/local/2dx

Installing for general use

• copied all of /usr/local/2dx to /cryoem/2dx_210, and made link: ln -s /cryoem/2dx_210 /cryoem/2dx
• copied all of /usr/local/Trolltech to /cryoem/Trolltech (QT4.3)
• copied libfftw libraries to /cryoem/fftw3/lib
• made links to correct libraries in /cryoem/2dx:

  cd /cryoem/2dx
  mkdir lib
  ln -s  /cryoem/Trolltech/Qt-4.3.2/lib/libQtCore.so.4 lib/.
  ln -s /cryoem/Trolltech/Qt-4.3.2/lib/libQtGui.so.4 lib/.
  ln -s /cryoem/Trolltech/Qt-4.3.2/lib/libQtNetwork.so.4 lib/.
  ln -s /cryoem/Trolltech/Qt-4.3.2/lib/libQtOpenGL.so.4 lib/.
  

• edit .cshrc as follows:

  setenv PATH $PATH:/cryoem/2dx/bin
  setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:/cryoem/2dx/lib:/cryoem/fftw3/lib
  

• edit /cryoem/2dx/config/2dx.cshrc as follows:

  source "/cryoem/CCP4/setup-scripts/csh/ccp4.setup"
  setenv DYLD_LIBRARY_PATH "/cryoem/2dx/lib:$DYLD_LIBRARY_PATH"
  

2DX v3

• installed version 3 April 21-22 2009
• Version 3 includes merging, bugfixes, other enhancements
• For CentOS5^? systems (cem03,cem12), binary worked with following additions:
  • recompiled fftw3 as shared library
  • installed precompiled QT 4.5 on each computer, under /usr/local
  • changed LD_LIBRARY_PATH to reflect new libraries
• on /cryoem/ , 2dx link now points to version 3
• For CentOS^? 4 system (cem02), precompiled version did not work
  • compiled QT 4.5 from scratch , installed under /usr/local/Trolltech
  • compiled fftw3 from scratch, installed under /usr/local/lib

options:
  --enable-shared
  --enable-single may be necessary for some applications

• • compiled 2dx from scratch, installed under /usr/local/2dx
    • compiling required editing: needed to edit one header from Trolltech, some headers in 2dx
    • more specifically, edited ./include/QtCore/qvariant.h to make the Qvariant public instead of private (near line 413)

2DX version 3, for 32-bit

• extracted files from precompiled .deb file on a debain-type machine using dpkg -x command
• retarred and transferred to course pc
• would not run -- wrong gcc

compile from source

FFTW3

• installed fftw 3.2.2 from /usr/local/src/fftw3.2.2/

                               ./configure --enable-shared --enable-single
                               make
                               make install
  

• installed into /usr/local/lib

QT 4.42

• install qlibrary 4.42 from Trolltech
• installed from /usr/local/src -- output is /usr/local/Trolltech
• installed using configure, qmake, qmake install -- no problems but took many hours

CCP4

• downloaded latest version plus all linraries from ccp4 site
• installed into /usr/local/src/ccp4
• make link from /usr/local/src/ccp4/ccp4-6.1.13/ to /usr/local/src/ccp4 [as per 2dx instructions]
• made link from /usr/local/src/ccp4/setup-scripts/csh/ccp4.setup to /usr/local/ccp4/bin/ccp4.setup.csh [as per 2dx instructions]

2dx

• downloaded source, put in /usr/local/src/2dx
• compile -- ./configure
• error with qmake
• FIX: edit path so qmake from qt4.4 is first in path:

         setenv PATH /usr/local/Trolltech/Qt-4.4.2/bin:$PATH

• now ./configure is ok
• make
• got error in periodogram.cpp about pthreads
• FIX: edit /usr/local/src/2dx/kernel/mrc/source/periodogram/Makefile as follows

         CFLAGS= -w -ffast-math -DUSE_THREADS_2DX -ffast-math -lpthread

• now compiles
• sudo make install
• installed into /usr/local/2dx

2dx July 2013

• Nicolas noted that 2dx does not work on any workstation (minotaur, zeus, orpheus)
• QT problems
• downloaded new libQt 4.6.3 (qt-everywhere-opensource-src-4.6.3.tar.gz from http://ftp.heanet.ie/mirrors/ftp.trolltech.com/pub/qt/source/)
• compiled on 64-bit CentOS^? 5 machine:

./configure -prefix /cryoem/qt_4.6.3 -no-phonon -no-phonon-backend -no-nis -no-openvg -nomake demos -nomake examples
gmake
gmake install

• adding /cryoem/qt_4.6.3/lib to $LD_LIBRARY_PATH allows currently installed 2dx to work

Compiling latest version of 2dx (3.4.1, April 2012, downloaded nightly version as that is the only one available)

• Compiled QT 4.6.3 as above
• Downloaded latest FFTW 3.3.3
• Compiled using

./configure --enable-shared --enable-single --enable-float --prefix=/cryoem/fftw-3.3.3
make
make install

• compile 2dx:
• Added above FFTW nad QT libraries to LD_LIBRARY_PATH
• compilation command:

./build_all ~/Downloads/2dx_nightly_source /cryoem/2dx_nightly_source_3.4.1_071013

• First try:

• complaint about KERNEL: Could not find libstdc++
  • • fix, similar to previous compilation, was:

           sudo ln -s /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libstdc++.a /usr/lib/.

• failure to find FFTW libraries
  • added variable DYLD_LIBRARY_PATH (used in MacOSX): did not fix
  • coped FFTW libraries to /usr/local/lib: partial success but still could not find header files
  • edited cmake/FindFFTW.cmake as follows (header location added at end):

IF(USE_FFTWD OR USE_FFTWF)

  SET(FFTW_INC_SEARCHPATH
    /sw/include
    /usr/include
    /usr/local/include
    /usr/include/fftw
    /usr/local/include/fftw
    /opt/local/include
    /programs/i386-mac/fftw/3.0.1/include
    /programs/i386-linux/fftw/3.3/include
    /cryoem/fftw-3.3.3/include
  )

• success!

• however, failure at following step:

| configure                                                                  |
cmake -DCMAKE_INSTALL_PREFIX=/cryoem/2dx_nightly_source_3.4.1_071013 -DAPPLE_BUNDLE=OFF /home/rice/Downloads/2dx_nightly_source
svn: '/home/rice/Downloads/2dx_nightly_source' is not a working copy
-- SVN dummy return: 1
-- No svn revision found
-- SVN revision number: unknown
-- The variable 2DX_ROOT_DIR is set to: /home/rice/Downloads/2dx_nightly_source
-- The variable 2DX_INCLUDE_DIR is set to: /home/rice/Downloads/2dx_nightly_source/include
-- Install prefix is set to /cryoem/2dx_nightly_source_3.4.1_071013
-- adding f95 specific flags
-- /home/rice/Downloads/2dx_nightly_source/kernel/mrc/lib/libmisc.a
-- KERNEL/LIB: Found QT4 at /cryoem/qt_4.6.3/lib
-- THE BUILD TYPE IS SET TO: RELEASE
-- adding f95 specific flags
-- adding gcc specific flags
-- KERNEL: Found stdc++ at /usr/lib/libstdc++.a
-- KERNEL: Found FFTW at /usr/local/lib/libfftw3f.so
-- THE BUILD TYPE IS SET TO: RELEASE
-- Included conf-1 Library
-- conf: Found QT4 at /cryoem/qt_4.6.3/lib
-- We are building the library at the moment
-- Included extentions-1 Library
-- extentions: Found QT4 at /cryoem/qt_4.6.3/lib
-- Included mrcImage-1 Library
-- mrcImage: Found FFTW at /usr/local/lib/libfftw3f.so
-- mrcImage: Found QT4 at /cryoem/qt_4.6.3/lib
-- Included widgets-1 Library
-- widgets: Found FFTW at /usr/local/lib/libfftw3f.so
-- widgets: Found QT4 at /cryoem/qt_4.6.3/lib
-- widgets: building at the moment
-- widgets: BINARY_DIR is /home/rice/Downloads/2dx_nightly_source/lib/src/widgets
-- CMAKE_PREFIX_PATH /home/rice/Downloads/2dx_nightly_source/share
-- 2dx_image: Found FFTW at /usr/local/lib/libfftw3f.so
-- 2dx_image: Found QT4 at /cryoem/qt_4.6.3/lib
-- 2dx_image: Found OpenGL at /usr/lib64/libGLU.so;/usr/lib64/libGL.so;/usr/lib64/libSM.so;/usr/lib64/libICE.so;/usr/lib64/libX11.so;/usr/lib64/libXext.so
-- Creating: 2dx_image
-- 2dx_merge: Found FFTW at /usr/local/lib/libfftw3f.so
-- Found QT4 at /cryoem/qt_4.6.3/lib
-- Found OpenGL at /usr/lib64/libGLU.so;/usr/lib64/libGL.so;/usr/lib64/libSM.so;/usr/lib64/libICE.so;/usr/lib64/libX11.so;/usr/lib64/libXext.so
-- Creating: 2dx_merge
-- 2dx_logbrowser: Found QT4 at /cryoem/qt_4.6.3/lib
-- Creating: 2dx_logbrowser
-- Configuring done
-- Generating done
-- Build files have been written to: /home/rice/Downloads/2dx_nightly_source

+----------------------------------------------------------------------------+
| make                                                                       |
[  0%] Built target plot2k
[  0%] Built target 2dx
[  1%] Built target fft
[  1%] Built target conv
[  1%] Built target fsplit
[  1%] Built target 2dx_CompleteFriedel
[  2%] Built target 2dx_DATAtranslate
[  2%] Built target 2dx_allspacea
[  2%] Built target 2dx_avrgamphs
[  2%] Built target 2dx_boximage
[  3%] Built target 2dx_calangle
[  3%] Built target 2dx_calc_num_phases
[  3%] Built target 2dx_calcmag
[  3%] Built target 2dx_calcpositions
[  4%] Built target 2dx_callat
[  4%] Built target 2dx_ccunbendh
[  4%] Built target 2dx_ccunbendk
[  4%] Built target 2dx_centric
[  5%] Built target 2dx_centric2
[  5%] Built target 2dx_centric3
[  5%] Built target 2dx_checklat3
[  5%] Built target 2dx_ctfapplyk
[  6%] Built target 2dx_ctfsearch2
[  6%] Built target 2dx_edmtz
[  6%] Built target 2dx_emtilt
[  6%] Built target 2dx_fftrans
[  7%] Built target 2dx_findlat
[  7%] Built target 2dx_getdirectories
[  7%] Built target 2dx_getnumber
[  7%] Built target 2dx_getspot
[  8%] Built target 2dx_hand
[  8%] Built target 2dx_hklclean
[  8%] Built target 2dx_hklsym
[  8%] Built target 2dx_hklsym2
[  9%] Built target 2dx_hklsym3
[  9%] Building Fortran object kernel/mrc/source/CMakeFiles/2dx_hklsym4.dir/2dx_hklsym4.for.o
 In file /home/rice/Downloads/2dx_nightly_source/kernel/mrc/source/2dx_hklsym4.for:921

        INTEGER, DIMENSION(3), allocatable :: MINDEX
                                         1
Error: Attribute at (1) is not allowed in a TYPE definition

• many more errors follow, of course
• apparently the gfortran in CentOS 5 does not understand syntax used for dynamic memory allocation in this program (too new?)

• CentOS 5 version (from gfortran-v) : gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)
• CentOS 6 version: gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC)
• Will retry in CentOS 6

• Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007