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LDAK is a command-line software, that can be run on either Linux or a Mac. I strongly recommend the Linux version, as it will often be much faster than the Mac version. LDAK does not run directly on Windows, so I suggest you instead log into a Linux server (for example, you can use putty to ssh into your local computer cluster). However, it is possible to instead use the Windows SubSystem for Linux (see Run LDAK on Windows for more information).
There are three ways to obtain LDAK; you can download the LDAK executable, you can install LDAK via conda, or you can compile your own version of LDAK from the source code.
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1A - Download the Linux executable:
(note that if using a MAC, you should instead follow the instructions in 1B)
Download and unzip the Linux executable file (link at the bottom)
Open a terminal window (on my Linux, I go to Applications / System Tools / Terminal)
Type the name of the file; for example
/home/doug/Downloads/ldak6.3.linux
or if you are in the same folder as the executable file, you can simply type
./ldak6.3.linux
If compatible with your system, this should produce the LDAK welcome screen. Note that if your computer tells you that you do not have permission to run the file, then first run
chmod a+x ldak6.3.linux
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1B - Download the MAC executable:
(note that if using Linux, you should instead follow the instructions in 1A)
Download and unzip the Mac executable file (link at the bottom)
Open a terminal window (go to Finder / Applications / Utilities)
Type the name of the file; for example
Downloads/ldak6.3.mac
or if you are in the same folder as the executable file, you can simply type
./ldak6.3.mac
If compatible with your system, this should produce the LDAK welcome screen. Note that if your computer tells you that you do not have permission to run the file, then first run
chmod a+x ldak6.3.mac
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2 - Install LDAK via conda (Linux systems only):
# create a new environment and install ldak6
conda create -n ldak_env -c genomedk ldak6
# load the new environment
conda activate ldak_env
# check ldak runs if you type the following
ldak6
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3A - Compile a Linux version of LDAK from source code:
(note that if using a MAC, you should instead follow the instructions in 3B)
The pre-compiled Linux version uses the Intel MKL Libraries. The command I used was
gcc --static -O3 -o ldak6.3.linux ldak/ldak.c ldak/libqsopt.linux.a -m64 -Wl,--start-group ${MKLROOT}/lib/libmkl_intel_lp64.a ${MKLROOT}/lib/libmkl_gnu_thread.a ${MKLROOT}/lib/libmkl_core.a -Wl,--end-group -lgomp -lpthread -lm -ldl -lz -I${MKLROOT}/include -fopenmp -L/home/doug/opt/lib -I/home/doug/opt/include
Should you wish to compile a Linux version yourself, please download and unzip the source code (link at the bottom), then from inside that folder run a command similar to
gcc -O3 -o ldak6.3 ldak.c libqsopt.linux.a -lblas -llapack -lm -lz -fopenmp
chmod a+x ldak6.3
The exact command will depend on which libraries you have installed. This should take less than a minute to complete. Note that if you do not have Intel MKL Libraries installed, you will be required to turn off the MKL libraries, by editing Line 63 of ldak.c (replace #define MKL 1 with #define MKL 0). If you are required to do this, then your self-compiled version will likely be slower than the pre-compiled version.
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3B - Compile a MAC version of LDAK from source code:
(note that if using Linux, you should instead follow the instructions in 3A)
To compile a Mac version yourself, please download and unzip the source code (link at the bottom), then from inside that folder run a command similar to
gcc -O3 -o ldak6.3.mac ldak.c libqsopt.mac.a -lblas -llapack -lm -lz
chmod a+x ldak6.3.mac
The exact command will depend on your system and which libraries you have installed. This should take about a minute to complete. Note that you will be required to turn off the MKL libraries, by replacing #define MKL 1 with #define MKL 0 (this code is located at approximately Line 54 in the file ldak.c). Further, it may be necessary to add -arch x86_64 to the above command, and/or to install xcode, by first running the command
xcode-select --install
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Latest LDAK Executables:
Use the links below to download the Linux and Mac versions of the LDAK executable (the link will take you to the corresponding GitHub page; you can then click the three dots, followed by Download). Note that the GitHub pages also contain a beta version of the Linux executable, but please only use this if instructed.
Click here to download ldak6.3.linux
Click here to download ldak6.3.mac
LDAK Source Code:
You can download the source code by visiting the LDAK GitHub pages, then downloading the file called Source_Code.zip.
