Difference: InstalL2DX (1 vs. 12)

Revision 1218 Jul 2013 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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

Added:

>
>

CentOS^? 6 compile

use built-in qt:

rpm -qa | grep qt
poppler-qt4-0.12.4-3.el6_0.1.x86_64
dbus-qt-0.70-7.2.el6.x86_64
qt-4.6.2-26.el6_4.x86_64
qt-mysql-4.6.2-26.el6_4.x86_64
qt3-3.3.8b-30.el6.x86_64
qt-mobility-1.1.3-2.el6.x86_64
qt-sqlite-4.6.2-26.el6_4.x86_64
qt-x11-4.6.2-26.el6_4.x86_64
ibus-qt-1.3.0-2.el6.x86_64
qt3-devel-3.3.8b-30.el6.x86_64
qtwebkit-devel-2.1.1-1.el6.x86_64
qt-doc-4.6.2-26.el6_4.noarch
qtwebkit-2.1.1-1.el6.x86_64
pinentry-qt-0.7.6-6.el6.x86_64
qt-devel-4.6.2-26.el6_4.x86_64

use built-in fftw:

rpm -qa | grep fft
fftw-devel-3.2.1-3.1.el6.x86_64
fftw-static-3.2.1-3.1.el6.x86_64
fftw-3.2.1-3.1.el6.x86_64

* newer gfortran works!

build command

./build_all /home/rice/2dx_nightly_source /usr/local/2dx/

Scanning dependencies of target 2dx_image
[ 80%] Building CXX object 2dx_image/CMakeFiles/2dx_image.dir/mainWindow.cpp.o
In file included from /home/rice/2dx_nightly_source/2dx_image/mainWindow.h:32,
                 from /home/rice/2dx_nightly_source/2dx_image/mainWindow.cpp:21:
/home/rice/2dx_nightly_source/2dx_image/centralWindow.h:25:20: error: QWebView: No such file or directory
In file included from /home/rice/2dx_nightly_source/2dx_image/centralWindow.h:36,
                 from /home/rice/2dx_nightly_source/2dx_image/mainWindow.h:32,
                 from /home/rice/2dx_nightly_source/2dx_image/mainWindow.cpp:21:
/home/rice/2dx_nightly_source/2dx_image/statusViewer.h:8:20: error: QWebPage: No such file or directory
/home/rice/2dx_nightly_source/2dx_image/statusViewer.h:9:21: error: QWebFrame: No such file or directory
In file included from /home/rice/2dx_nightly_source/2dx_image/centralWindow.h:36,
                 from /home/rice/2dx_nightly_source/2dx_image/mainWindow.h:32,
                 from /home/rice/2dx_nightly_source/2dx_image/mainWindow.cpp:21:
/home/rice/2dx_nightly_source/2dx_image/statusViewer.h:17: error: expected class-name before ‘{’ token
make[2]: *** [2dx_image/CMakeFiles/2dx_image.dir/mainWindow.cpp.o] Error 1
make[1]: *** [2dx_image/CMakeFiles/2dx_image.dir/all] Error 2
make: *** [all] Error 2
Build failed for 2dx

No QT webkit!
install QT-webkit:

sudo yum install qtwebkit-devel

success!!!

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Added:

>
>

Revision 1118 Jul 2013 - Main.BillRice

   META TOPICPARENT   name="CemIT" 

Contents
 
 2DX Installation 
  2DX v2
  Installed fftw3
   Install QT 4.3
   Install CCP4
   Compile 2dx
  Installing for general use
   2DX v3
   2DX version 3, for 32-bit
   compile from source
  FFTW3 
 QT 4.42
 
   CCP4
   2dx
   2dx July 2013
 
 


 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
-  META TOPICPARENT
+ name="CemIT"
-<
<
+qmake
qmake install
->
>
+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
-<
<

Revision 1018 Jul 2013 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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
qmake
qmake install

Changed:

<
<

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

>
>

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

Added:

>
>

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

Revision 912 Jul 2013 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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

Added:

>
>

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
qmake
qmake install

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

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Added:

>
>

Revision 826 Nov 2010 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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

Changed:

<
<

compile form source

>
>

compile from source

Added:

>
>

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
Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Revision 726 Nov 2010 - Main.BillRice

   META TOPICPARENT   name="CemIT" 

Contents
 
 2DX Installation 
  2DX v2
  Installed fftw3
   Install QT 4.3
   Install CCP4
   Compile 2dx
  Installing for general use
   2DX v3
   2DX version 3, for 32-bit
   compile form source 
 QT 4.42
 
   CCP4
   2dx
 
 


 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 form source 

 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:
-  META TOPICPARENT
+ name="CemIT"
-<
<
+      setenv PATH /usr/local/Trolltech/Qt-4.4.2/bin:$PATH
->
>
+         setenv PATH /usr/local/Trolltech/Qt-4.4.2/bin:$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
->
>
+         CFLAGS= -w -ffast-math -DUSE_THREADS_2DX -ffast-math -lpthread
  now compiles
-<
<
->
>
+ sudo make install
->
>
+ installed into /usr/local/2dx
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 14 Nov 2007

Revision 626 Nov 2010 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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)

Added:

>
>

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 form source

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

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Revision 509 Jun 2010 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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

Added:

>
>

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)

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Revision 406 Oct 2009 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

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
- compiled 2dx from scratch, installed under /usr/local/2dx
  - compiling required editing: needed to edit one header from Trolltech, some headers in 2dx

Changed:

<
<

>
>

- - more specifically, edited ./include/QtCore/qvariant.h to make the Qvariant public instead of private (near line 413)

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Revision 322 Apr 2009 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

2DX Installation

Added:

>
>

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"

Added:

>
>

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
- compiled 2dx from scratch, installed under /usr/local/2dx
  - compiling required editing: needed to edit one header from Trolltech, some headers in 2dx

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Revision 214 Nov 2007 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation
- Installed fftw3
- Install QT 4.3

2DX Installation

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

Added:

>
>

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
```

Added:

>
>

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"

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

Revision 114 Nov 2007 - Main.BillRice

META TOPICPARENT	name="CemIT"

Contents

2DX Installation

2DX Installation

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

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
```

Set ALLOWTOPICVIEW =

-- BillRice - 14 Nov 2007

View topic | History: r12 < r11 < r10 < r9 | More topic actions...

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Difference: InstalL2DX (1 vs. 12)

Revision 1218 Jul 2013 - Main.BillRice

2DX Installation

2DX v2

Installed fftw3

Install QT 4.3

Install CCP4

Compile 2dx

Installing for general use

2DX v3

2DX version 3, for 32-bit

compile from source

FFTW3

QT 4.42

CCP4

2dx

2dx July 2013

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

CentOS? 6 compile

Revision 1118 Jul 2013 - Main.BillRice

2DX Installation

2DX v2

Installed fftw3

Install QT 4.3

Install CCP4

Compile 2dx

Installing for general use

2DX v3

2DX version 3, for 32-bit

compile from source

FFTW3

QT 4.42

CCP4

2dx

2dx July 2013

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

Revision 1018 Jul 2013 - Main.BillRice

2DX Installation

2DX v2

Installed fftw3

Install QT 4.3

Install CCP4

Compile 2dx

Installing for general use

2DX v3

2DX version 3, for 32-bit

compile from source

FFTW3

QT 4.42

CCP4

2dx

2dx July 2013

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

Revision 912 Jul 2013 - Main.BillRice

2DX Installation

2DX v2

Installed fftw3

Install QT 4.3

Install CCP4

Compile 2dx

Installing for general use

2DX v3

2DX version 3, for 32-bit

compile from source

FFTW3

QT 4.42

CCP4

2dx

2dx July 2013

Revision 826 Nov 2010 - Main.BillRice

2DX Installation

2DX v2

Installed fftw3

Install QT 4.3

Install CCP4

Compile 2dx

Installing for general use

2DX v3

2DX version 3, for 32-bit

compile form source

CentOS^? 6 compile