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| ===== Quick start ===== | ===== Quick start ===== | ||
| - | - Download the latest version from the website | + | * Download the latest version from the website |
| - | - Uncompress the archive downloaded | + | * Uncompress the archive downloaded |
| - | - Move the directory to the directory where you want to install the programs | + | * Move the directory to the directory where you want to install the programs |
| - | - Open a terminal and launch the installation script | + | * Open a terminal and launch the installation script <code> |
| - | + | ./auto3dem_install | |
| - | Linux | + | </code> |
| - | make_all [serial | parallel] [all | gui | nogui] | + | * The script will detect the platform and by default will build all the applications, including those based on a graphical user interface (GUI), assuming the GNU compilers are available. The computing-intensive codes are parallelized using MPI, and the parallel version is compiled by default. You can change the default settings by adding specific options. For a complete list of them type ''./auto3dem_install --help'' |
| - | Mac OSX | + | |
| - | mac_make_all [serial | parallel] [all | gui | nogui] | + | * Provide path information for binaries and perl scripts. For example, C shell users should add the following to your .cshrc file, where x.xx is the auto3dem version. <code> |
| - | Choose serial or parallel to build image reconstruction codes that run | + | set path = (/path_to_auto3dem/auto3dem_vx.xx/bin $path) |
| - | in serial or parallel mode, respectively. All parallelization is done | + | </code> Of course, it's probably more convenient to create a symbolic link named auto3dem that points to the latest version. |
| - | using MPI. The second option specifies whether all, only GUI-based, or | + | |
| - | only non-GUI based applications should be built. | + | |
| - | \\ | + | |
| - | You will generally want to build the entire suite, but these options | + | |
| - | are provided both for developers and those who may not have all of the | + | |
| - | necessary Motif libraries for the GUIs. | + | |
| - | + | ||
| - | __NOTES__: | + | |
| - | * For serial mode, the FC and CC macros in the make.inc.serial file point to the gfortran and gcc compilers, respectively. You will need to edit this file if you are using other compilers. | + | |
| - | * For parallel mode, the FC and CC macros in the make.inc.parallel file point to the mpif90 and mpicc scripts, respectively. You will need to edit this file if you are using other compilation scripts. | + | |
| - | * In the future we hope to develop a more robust build system, but for now you're stuck having to do some of the work on your own if using other compilers. | + | |
| - | - Provide path information for binaries and perl scripts. For example, C shell users should add the following to your .cshrc file, where x.xx is the auto3dem version. | + | |
| - | + | ||
| - | set path = (/path_to_auto3dem/auto3dem_vx.xx/bin $path) | + | |
| - | + | ||
| - | Of course, it's probably more convenient to create a symbolic link | + | |
| - | named auto3dem that points to the latest version. | + | |
| + | ===== Compilers ===== | ||
| + | The installation script assumes that GNU compilers are available on the computer and will try to compile the programs using those. If you want to use different compilers, you can specify them with the option //--compiler//. The settings for some compilers are already available, and the option //--help// provides a list of them. You can add the settings for a compiler that is not listed by adding a file for the specific combination you intend to use (platform, compiler, parallel or serial) in the //Make// directory, using the ones already present as templates. | ||
| ===== Library dependencies ===== | ===== Library dependencies ===== | ||
| - | |||
| AUTO3DEM does not depend on external programs, but relies on libraries of the operating system that are not necessarily present by default. | AUTO3DEM does not depend on external programs, but relies on libraries of the operating system that are not necessarily present by default. | ||
| - | - libraries needed for running the programs in parallel using MPI | + | * [[auto3dem:installation:linux_libraries|Linux]] |
| - | openmpi (mpich2 as an alternative) | + | * [[auto3dem:installation:macosx_libraries|Mac OSX]] |
| - | openmpi-devel (mpich2-devel as an alternative) | + | |
| - | - libraries needed for running graphical programs (mainly Robem) | + | |
| - | libX11 | + | |
| - | libX11-devel | + | |
| - | openmotif | + | |
| - | openmotif-devel | + | |
| - | libSM | + | |
| - | libSM-devel | + | |
| - | libICE | + | |
| - | libICE-devel | + | |
| - | libXext | + | |
| - | libXext-devel | + | |
| - | libXmu | + | |
| - | libXmu-devel | + | |
| - | libXp | + | |
| - | libXp-devel | + | |
| - | libXt | + | |
| - | libXt-devel | + | |
| + | ===== Python requirements ===== | ||
| + | |||
| + | The python programs provided should run on Python version 2.3 and older. | ||
| + | The program to plot one or multiple FSC curves, //a3dm_plot_fsc.py//, requires the modules //Numpy// and //Matplotlib//, which usually are not installed by default but are available from the package manager of most Linux distributions. | ||
| ===== Perl requirements ===== | ===== Perl requirements ===== | ||
| - | + | //auto3dem// and the auxilliary routines //setup_rmc//, //handflip//, | |
| - | auto3dem and the auxilliary routines setup_rmc, handflip, | + | //remove_useless//, and //findbest// were developed using Perl version 5.8.5, |
| - | remove_useless, and findbest were developed using Perl version 5.8.5, | + | |
| but will probably run using slightly older versions. It is expected | but will probably run using slightly older versions. It is expected | ||
| that you have the standard set of CPAN modules, including Cwd, | that you have the standard set of CPAN modules, including Cwd, | ||
| Line 73: | Line 42: | ||
| FSC curves. | FSC curves. | ||
| + | ===== Running parallel jobs ===== | ||
| - | ===== Email notification ===== | + | AUTO3DEM currently is capable to run under the PBS and SGE batch schedulers. In |
| + | your job script, you will need to include the flag (-V) that exports | ||
| + | all environment variables to the job. Do not explicitly include a | ||
| + | nodefile in the auto3dem command since it is automatically passed | ||
| + | through the Perl %ENV hash. | ||
| + | If you are running on a system that is not under control of a batch | ||
| + | scheduler, you can specify that particular nodes be used with the | ||
| + | -nodefile flag. Depending on your computing environment, specification | ||
| + | of a nodefile may not be necessary. | ||
| - | auto3dem has the capability to send email notifications at the end of | + | ===== Email notification ===== |
| - | each iteration. Add the following line to your auto3dem input file | + | |
| + | auto3dem has the capability to send email notifications at the end of | ||
| + | each iteration. Add the following line to your auto3dem input file <code> | ||
| auto recipient address1 [address2 ...] | auto recipient address1 [address2 ...] | ||
| + | </code> | ||
| In order for this to work correctly, you will need to have the mutt | In order for this to work correctly, you will need to have the mutt | ||
| email program installed and properly configured. | email program installed and properly configured. | ||
| - | ===== Compiling image reconstruction codes ===== | + | ===== Additional notes ===== |
| + | ==== Compiling image reconstruction codes ==== | ||
| Line 96: | Line 76: | ||
| In order to build the executables, you will need the following | In order to build the executables, you will need the following | ||
| - | o Fortran 90 compiler | + | Fortran 90 compiler |
| - | o ANSI C compiler | + | ANSI C compiler |
| - | o MPI implementation (parallel mode only) | + | MPI libraries (parallel mode only) |
| - | + | ||
| - | The codes make extensive use of Fortran 90 features - dynamic memory | + | |
| - | management, newer intrinsic functions, array syntax, etc. - and will | + | |
| - | not compile under Fortran 77. | + | |
| Our codes have been successfully compiled and run using the gfortran | Our codes have been successfully compiled and run using the gfortran | ||
| and ifort Fortran compilers, the icc and gcc C compilers, and | and ifort Fortran compilers, the icc and gcc C compilers, and | ||
| - | MPICH2. That said, we expect that any standard compilers and MPI | + | the MPICH2 and openMPI libraies. That said, we expect that any standard compilers and MPI |
| implementation will work. | implementation will work. | ||
| - | To create binaries of the image reconstruction codes, simply execute | + | To create binaries of the image reconstruction codes, simply launch the installation script. This |
| - | 'make_all mode' (mode = parallel or serial) on the command line. This | + | |
| script sets symbolic links to the appropriate make include and perl | script sets symbolic links to the appropriate make include and perl | ||
| module files, enters each of the program and library directories, and | module files, enters each of the program and library directories, and | ||
| Line 116: | Line 91: | ||
| directory. | directory. | ||
| - | The make.inc.serial and make.inc.parallel files specify the compilers | + | ==== Programs providing a graphical user interface ==== |
| - | and flags that will be used by the Makefiles. These are fairly generic | + | |
| - | and may need to be manually edited if you are using anything other | + | |
| - | than the GNU compilers. | + | |
| - | + | //RobEM//, //fixpif//, //oned//, and //ctfdisp// all make use of the **Motif** graphical | |
| - | ===== Compiling image preprocessing applications ===== | + | |
| - | + | ||
| - | + | ||
| - | RobEM, fixpif, oned, and ctfDisp all make use of the Motif graphical | + | |
| user interface toolkit. You will need to install the appropriate | user interface toolkit. You will need to install the appropriate | ||
| library if you wish to use these programs. | library if you wish to use these programs. | ||
| Line 155: | Line 123: | ||
| % unsetenv LANG | % unsetenv LANG | ||
| - | ===== Running parallel jobs ===== | ||
| - | |||
| - | AUTO3DEM currently runs under the PBS and SGE batch schedulers. In | ||
| - | your job script, you will need to include the flag (-V) that exports | ||
| - | all environment variables to the job. Do not explicitly include a | ||
| - | nodefile in the auto3dem command since it is automatically passed | ||
| - | through the Perl %ENV hash. | ||
| - | |||
| - | If you are running on a system that is not under control of a batch | ||
| - | scheduler, you can specify that particular nodes be used with the | ||
| - | -nodefile flag. Depending on your computing environment, specification | ||
| - | of a nodefile may not be necessary. | ||