Using & Installing So:ware on Odyssey

Transcription

1 Using & Installing So:ware on Odyssey Bob Freeman, PhD Dir. Research Technology Opera1ons (HBS) formerly RC Facilitator Slide 1

2 Goals Objec&ves Feel knowledgeable about compute & so:ware environment Understand and create Lmod module files Know how to handle different types of programs & scripts Customize libraries for common scrip1ng languages Understand basics on so:ware development Know common prac1ces for compiling so:ware Strategically Work smarter, bever, faster... and to Think Differently Enable you to be successful with your research! Slide 2

3 Overview 1. Environment basics Login scripts & environment variables 2. Module system How they work, what they look like, and what they do for you 3. Crea1ng your own modules 4. Java, Python, & Perl applica1ons 5. Upda1ng local modules & packages 6. Version control 7. Using FASRC / precompiled libraries 8. Compiling So:ware Methods Flags, op1ons, and environment variables Troubleshoo1ng Slide 3

4 Environment basics When you login, Unix executes certain steps for your interac1ve sessions Startup files are read Command prompts are set up Aliases expanded. Startup files set up default values for your environment /etc/profile.bash_profile.bash_login.profile.bashrc The only things that really need to be in.bash_profile are environment variables and their exports and commands these aren t defini1ons but actually run or produce out- put when you log in. Op1on and alias defini1ons should go into the environment file (.bashrc) Slide 4

5 Environment basics ~]$ cat ~/.bash_profile #.bash_profile # Get the aliases and functions if [ -f ~/.bashrc ]; then. ~/.bashrc fi # User specific environment and startup programs How shells behave: Slide 5 a b c Shell: source alice hatter gryphon Shell: Subshell: Shell: Subshell: alice alice & Figure 4-1. Ways to run a shell script hatter hatter gryphon gryphon Chapter 3: Learning the bash Shell (O'Reilly) source.bash_profile & more, keeps all sekngs in same context main shell waits; subshell gets.bashrc only, knows about exports; all is lost a:er exit same as b, but main shell can keep doing work with other in bkg

6 Environment Basics ~]$ cat ~/.bashrc #.bashrc # Source global definitions if [ -f /etc/bashrc ]; then. /etc/bashrc fi # User specific aliases and functions command aliases alias l.='ls -d.*' alias lt='ls -alt' alias lthead='ls -alt head' alias llhead='ll head' alias which='alias /usr/bin/which --tty-only --read-alias --show-dot --show-tilde' alias get_interact1='srun --pty --x11=first --mem=1000 -p interact -t 0-6:00 /bin/bash' alias ssqueue='/usr/bin/squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %C"' alias sacct_ram="sacct --format=jobid,jobname,reqmem,maxrss,elapsed" alias cd_regal='cd /n/regal/rc_admin/bfreeman' export PATH=$PATH:$HOME/bin export PATH=$PATH:$HOME/apps/parafly/bin source new-modules.sh module load fasrc export EDITOR=nano adding executables to where systems looks op1ng in to new modules sekng default editor # setup local Perl environment export LOCALPERL=$HOME/apps/perl export PERL5LIB=$LOCALPERL:$LOCALPERL/lib/perl5:$PERL5LIB export PERL_MM_OPT="INSTALL_BASE=$LOCALPERL" export PERL_MP_OPT="--install_base $LOCALPERL" export PATH="$LOCALPERL/bin:$PATH" module load perl-modules # setup for local Python environment Slide 6 personal perl modules

7 Common Environment Variables You may run across these in your Unix & cluster endeavors... For variables that include filesystem loca1on (paths), these are colon (':') delimited, and usually do not contain a trailing '/'. Order is important! Pre- pending your local paths will supersede system executables of the same name Variable PATH Explana&on Ordered loca1ons that the system looks for programs you wish to execute HOME TEMP TMP TMPDIR DISPLAY EDITOR Your home folder. Usually not a good idea to change Local directory used for temporary file crea1on Used to direct X11 GUI data to the appropriate drawing screen The name of the user's preferred text editor. Used by command- line programs such as git LIBRARY_PATH LD_LIBRARY_PATH CLASSPATH PWD USER PAGER List of directories in which library files should be searched for List of directories for Java jar files / class files Your current directory Your account / login name Name of the u1lity used to display long text by commands such as man Slide 7

8 Overview 1. Environment basics Login scripts & environment variables 2. Module system How they work, what they look like, and what they do for you 3. Crea1ng your own modules 4. Java, Python, & Perl applica1ons 5. Upda1ng local modules & packages 6. Version control 7. Using FASRC / precompiled libraries 8. Compiling So:ware Methods Flags, op1ons, and environment variables Troubleshoo1ng Slide 8

9 Lmod Module System So:ware is loaded incrementally using modules, to set up your shell environment (e.g. PATH, BLASTDB, and other environment variables) Using the Harvard- modified, TACC module system Lmod: New system is s1ll opt- in. Strongly suggested reading: hvp://fasrc.us/rclmod source new-modules.sh module load fastqc/1.0.0-fasrc01 module load fastqc # for opt-in folks # recommended!! # most recent version module-query fastqc # recommended!! module-query --full-text fastqc # gives more detail module spider fastqc # find details on software module avail 2>&1 grep -i fastqc # find titles/defaults So:ware search capabili1es similar to module-query are also available on the RC Portal! Module loads best placed in SLURM batch scripts: Keeps your interac1ve working environment simple Is a record of your research workflow (reproducible research!) Keep.bashrc module loads sparse, lest you run into so:ware and library conflicts Slide 9 hvp://fasrc.us/rclmod

10 Lmod Module System LMod: Environmental Modules System from hvps:// development/tacc- projects/lmod Provide a convenient way to dynamically change the users' environment through modulefiles (Lua- based scrip1ng file). This includes easily adding or removing directories to the PATH environment variable. A modulefile contains the necessary informa1on to allow a user to run a par1cular applica1on or provide access to a par1cular library. dynamically changes environment without logging out and back in. applica1ons modify the user's path to make access easy. Library packages provide environment variables that specify where the library and header files can be found. Packages can be loaded and unloaded cleanly through the module system. All the popular shells are supported: bash, ksh, csh, tcsh, zsh. Also available for perl and python. It is also very easy to switch between different versions of a package or remove it. Slide 10 hvp://fasrc.us/rclmod

11 Modules: How do they work?(1) ~]$ module load trinity/2.0.6-fasrc01 ~]$ which Trinity /n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/trinity ~]$ ll /n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01 total 974 drwxr-xr-x 12 root root 514 May drwxr-xr-x 7 root root 163 Oct 30 12:51.. drwxr-xr-x 5 root root 118 May Analysis drwxr-xr-x 4 root root 171 May Butterfly drwxr-xr-x 9 root root 1488 May Chrysalis drwxr-xr-x 2 root root 695 May galaxy-plugin drwxr-xr-x 3 root root 540 May hpc_conf drwxr-xr-x 4 root root 501 May Inchworm -rw-r--r-- 1 root root 1490 May LICENSE -rw-r--r-- 1 root root 1492 May LICENSE.txt -rw-r--r-- 1 root root 1737 May Makefile -rw-r--r-- 1 root root 2113 May modulefile.lua -rw-r--r-- 1 root root 87 May notes drwxr-xr-x 7 root root 1384 May PerlLib -rw-r--r-- 1 root root 105 May README -rw-r--r-- 1 root root 76 May README.md -rw-r--r-- 1 root root May Release.Notes drwxr-xr-x 12 root root 444 May sample_data -rwxr-xr-x 1 root root May Trinity drwxr-xr-x 11 root root 620 May trinity-plugins drwxr-xr-x 7 root root 634 May util [bfreeman@sa01 ~]$ pushd!$ # cool: save current dir and use last param of last cmd pushd /n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01 /n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01 ~/source_tarballs ~ Slide 11

12 Modules: How do they work? (2) fasrc01]$ cat modulefile.lua local helpstr = [[ trinityrnaseq fasrc01 De-novo assembler from RNA-Seq from Broad Inst. et al. ]] help(helpstr,"\n") whatis("name: trinityrnaseq") whatis("version: fasrc01") whatis("description: De-novo assembler from RNA-Seq from Broad Inst. et al.") info for module- query & help program metadata ---- prerequisite apps (uncomment and tweak if necessary) for i in string.gmatch("bowtie/1.1.1-fasrc01 samtools/1.1-fasrc02 perl-modules/ fasrc11","%s+") do if mode()=="load" then a = string.match(i,"^[^/]+") if not isloaded(a) then load(i) end end end ---- environment changes (uncomment what is relevant) prepend_path("path", "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01") setenv("trinity_home", "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01") we load dependencies for you Magic! we change your environment as needed --prepend_path("cpath", --prepend_path("fpath", --prepend_path("infopath", --prepend_path("ld_library_path", --prepend_path("library_path", --prepend_path("ld_library_path", --prepend_path("library_path", --prepend_path("manpath",... "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/include") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/include") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/info") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/lib") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/lib") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/lib64") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/lib64") "/n/sw/fasrcsw/apps/core/trinityrnaseq/2.0.6-fasrc01/man") Slide 12

13 Modules: Why Use Hierarchies? Use of groupings is important for proper func1oning programs! Libraries built with one compiler need to be linked with applica1ons with the same compiler version. For HPC there are libraries called Message Passing Interface (MPI) that allow for efficient communica1ng between tasks on a distributed memory computer with many processors. Parallel libraries and applica1ons must be built with a matching MPI library and compiler. Instead of using a flat namespace, we can use module hierarchies! Simple technique because once users choses a compiler and MPI implementa1on, they can only load modules that match that compiler and MPI implementa1on. FASRC follow's TACC's conven1on: $MODULEPATH_ROOT/{Core,Comp,MPI} # /n/sw/fasrcsw/modulefiles Core: Comp: MPI: compiled so:warelibraries that should work in all environments so:ware/libraries 1ed to a specific compiler and version compiler- specific & MPI- specific flavors of so:ware/libraries Slide 13

14 Modules: Hierarchies modulefiles]$ module-query raxml raxml Description: RAxML (Randomized A(x)ccelerated Maximum Likelihood) is a program for sequential and parallel Maximum-Likelihood-based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. It has originally been derived from fastdnaml which in turn was derived from Joe Felsentein s dnaml which is part of the PHYLIP package. Versions: raxml/8.1.5-fasrc03... Comp raxml/8.1.5-fasrc02... MPI raxml/7.7.6.bib-fasrc02... Core raxml/7.3.0-fasrc01... Core To find detailed information about a module, enter the full name. For example, module-query raxml/7.3.0-fasrc01 Slide 14

15 Modules: Hierarchies modulefiles]$ module-query raxml/8.1.5-fasrc raxml : raxml/8.1.5-fasrc Description: RAxML (Randomized A(x)ccelerated Maximum Likelihood) is a program for sequential and parallel Maximum-Likelihood-based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. It has originally been derived from fastdnaml which in turn was derived from Joe Felsentein s dnaml which is part of the PHYLIP package. Build comments: Building with SSE3 instructions. Some, but not all compute nodes have AVX. Spec file can be used properly as either Comp or MPI. When building as Comp, the CC line is removed from the Makefile so that the environment value is picked up. This module an be loaded as follows: module load gcc/4.8.2-fasrc01 openmpi/1.8.1-fasrc04 raxml/8.1.5-fasrc02 module load gcc/4.8.2-fasrc01 openmpi/ fasrc01 raxml/8.1.5-fasrc02 module load gcc/4.8.2-fasrc01 openmpi/1.8.3-fasrc02 raxml/8.1.5-fasrc02 module load gcc/4.8.2-fasrc01 mvapich2/2.0-fasrc03 raxml/8.1.5-fasrc02 module load gcc/4.8.2-fasrc01 mvapich2/2.0-fasrc02 raxml/8.1.5-fasrc02 module load intel/ fasrc01 openmpi/1.8.1-fasrc04 raxml/8.1.5-fasrc02 module load intel/ fasrc01 openmpi/ fasrc01 raxml/8.1.5-fasrc02 module load intel/ fasrc01 openmpi/1.8.3-fasrc02 raxml/8.1.5-fasrc02 module load intel/ fasrc01 mvapich2/2.0-fasrc03 raxml/8.1.5-fasrc02 module load intel/ fasrc01 mvapich2/2.0-fasrc02 raxml/8.1.5-fasrc02 [bfreeman@sa01 modulefiles]$ module load gcc/4.8.2-fasrc01 openmpi/ fasrc01 raxml/8.1.5-fasrc02 [bfreeman@sa01 modulefiles]$ which raxml /n/sw/fasrcsw/apps/mpi/gcc/4.8.2-fasrc01/openmpi/ fasrc01/raxml/8.1.5-fasrc02/bin/raxml Slide 15

16 Modules: Make your own! Why? Install newer version of open source so:ware than is currently available in central loca1ons Easily change version of applica1ons or libraries while being developed BeVer documenta1on for what so:ware is available. It is easy to install a new version of some sodware and place it in your personal PATH and forget about it. At least when it is in a module, it be listed in the loaded modules. Can be done in 3 easy steps 1. Add loca1on of local module files to module path 2. Create the module file with lua code for the appropriate program/package 3. Do the new module load (Voila!) 4. Include the op1onal modules path in your.bashrc login script Slide 16 hvps:// development/tacc- projects/lmod/advanced- user- guide

17 Modules: Make Your Own! # assumes that program & packages are in $HOME/apps [bfreeman@sa01 ~]$ ll apps/thin_fastq-1.0.0/ total 232 drwxr-xr-x 4 bfreeman rc_admin 46 Jan 26 08:41. drwxr-xr-x 17 bfreeman rc_admin 932 Jan 27 11:18.. drwxr-xr-x 3 bfreeman rc_admin 905 Jan 29 10:03 bin drwxr-xr-x 3 bfreeman rc_admin 32 Jan 26 08:41 include drwxr-xr-x 3 bfreeman rc_admin 905 Jan 29 10:03 lib # prepends your path to MODULEPATH environment variable. Can locate these anywhere. $ mkdir $HOME/modulefiles $ module use $HOME/modulefiles # assuming a program thin_fastq at $HOME/apps/thin_fastq-1.0.0/bin $ cd ~/modulefiles $ mkdir thin_fastq $ cd!$ # module file gets home directory from the environment # then uses Lmod 'pathjoin' function to join strings together # to pre-pends this program's location to the user's PATH $ cat > lua local home = os.getenv("home") local pkg = pathjoin(home,"apps/thin_fastq-1.0.0/bin") prepend_path("path", pkg) ^D # now load in the new module $ module load thin_fastq # this line will add the local (user) module environment for future logins $ echo 'module use $HOME/modulefiles' >> ~/.bashrc Slide 17

18 Overview 1. Environment basics Login scripts & environment variables 2. Module system How they work, what they look like, and what they do for you 3. Crea1ng your own modules 4. Java, Python, & Perl applica1ons 5. Upda1ng local modules & packages 6. Version control 7. Using FASRC / precompiled libraries 8. Compiling So:ware Methods Flags, op1ons, and environment variables Troubleshoo1ng Slide 18

19 Java Programs FASRC will no longer install Java apps and Python scripts they will probably not work correctly in read- only sec1ons of the cluster Python scripts use pip-install or python setup.py & doesn t work with some setups For Java Download the *.jar files or the install files into a home or lab apps/ or bin/ directory Include the java CLASSPATH statement in your.bashrc, OR Set up a bash environment variable in your.bashrc Call the so:ware using the java command, poin1ng to the appropriate rou1ne cd ~ mkdir p apps; cd apps wget longurl /Trimmomatic-0.36.zip unzip Trimmomatic-0.36.zip ln s Trimmomatic-0.36 trimmomatic export TRIMMOMATIC=$HOME/apps/trimmomatic echo 'export TRIMMOMATIC=$HOME/apps/trimmomatic' >> ~/.bashrc # in SLURM script or on command line module load java/1.8.0_45-fasrc01 cd ~/myfastqdirectory; mkdir trimmed # minheap (-Xms) and maxheap (-Xmx) options are optional but useful in some cases!! java -Xms128m Xmx4g -jar $TRIMMOMATIC/trimmomatic-0.32.jar SE -threads 1 \ PSG177_TGACCA.fastq.gz trimmed/psg177_tgacca.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15 LEADING:3 TRAILING:3 \ SLIDINGWINDOW:4:20 MINLEN:25 Slide 19 hvp://fasrc.us/installsw

20 Python Programs For Python we recommend: Use the standard module load python/2.7.6-fasrc01 for pulling in default modules Use the Anaconda environment for customizing modules & versions Mul1ple custom environments can be set up for home or lab folders (e.g. development or produc1on code). Check conda op1ons for 'non- standard' loca1ons module load python/2.7.6-fasrc01 # for any python version conda create -n ENV_NAME --clone="$python_home # created at ~/env/env_name # load in environment source activate ENV_NAME # load in new package conda install MYPACKAGE # local environment is default # replace MYPACKAGE # update a specific package # 'remove' first if you hit update problems conda update MYPACKAGE # other methods after source activate pip install MYPACKAGE python setup.py install MYPACKAGE Slide 20 hvp://fasrc.us/installsw

21 R / Python / Perl Libraries We've already covered Python libraries. R and Perl are much simpler! R: Use the R_LIBS_USER environment variable # load R, default packages, & set local install dir (must already exist!) module load R_packages/3.2.0-fasrc01... # can put this in.bashrc, but best to do this after R module load export R_LIBS_USER=$HOME/apps/R:$R_LIBS_USER # R install.packages('deplyr') # inside R For Perl, we can do the same thing! # load Perl, default modules, & set local install dir (must already exist!) module load perl-modules/ fasrc11 # can put these in your.bashrc export LOCALPERL=$HOME/apps/perl export PERL5LIB=$LOCALPERL:$LOCALPERL/lib/perl5:$PERL5LIB export PERL_MM_OPT="INSTALL_BASE=$LOCALPERL" export PERL_MB_OPT="--install_base $LOCALPERL" export PATH="$LOCALPERL/bin:$PATH" # and now do easy, local installs with cpan cpan FASTAParse Slide 21 hvp://fasrc.us/installsw

22 Overview 1. Environment basics Login scripts & environment variables 2. Module system How they work, what they look like, and what they do for you 3. Crea1ng your own modules 4. Java, Python, & Perl applica1ons 5. Upda1ng local modules & packages 6. Version control 7. Using FASRC / precompiled libraries 8. Compiling So:ware Methods Flags, op1ons, and environment variables Troubleshoo1ng Slide 22

23 Version Control Version control is a system that records changes to a file or set of files over 1me so that you can recall specific versions later. Typically used for source code files In reality you can do this with nearly any type of file on a computer. Slide 23 from Git SCM book

24 Installing Your Own Software Users can compile so:ware in their /home or /groups directory, where they have permission Binaries just require unzipping (ie tar -zxvf *.tgz) Common compiling libraries are found as modules: gcc/4.8.2-fasrc01 intel/ fasrc01 boost/ fasrc01 gcc/4.8.2-fasrc01 llvm/3.5.1-fasrc02 gcc/4.8.2-fasrc01 openmpi/1.8.3-fasrc02 gcc/4.8.2-fasrc01 mvapich2/2.0-fasrc03 Common math libraries are also present but may be compiler- specific gcc/4.8.2-fasrc01 intel-mkl/ fasrc01 Slide 24 hvp://fasrc.us/installsw

25 Installing A Binary (Pre-compiled) Users can place so:ware in their /home or /groups directory, where they have permission Binaries just require unzipping (ie tar - zxvf.tgz) cd ~ mkdir p apps; cd apps wget longurl /mybinarysoftware-1.0.tgz tar -xvf mybinarysoftware-1.0.tgz ls mybinarysoftware-1.0 ln s mybinarysoftware-1.0 mybinarysoftware # add to.bashrc; assumes all binaries are in top level of this folder echo 'export PATH=$HOME/apps/myBinarySoftware:$PATH' >> ~/.bashrc export PATH=$HOME/apps/myBinarySoftware:$PATH # and now run it! mybinary Slide 25 hvp://fasrc.us/installsw

26 Installing From Source Code Users can compile so:ware in their /home or /groups directories, where they have permission Source requires untaring and (o:en) selec1ng a compiler cd ~ mkdir p apps; cd apps wget longurl /mybinarysoftware-1.0.tgz tar -xvf mybinarysoftware-1.0.tgz ls mybinarysoftware-1.0 ln s mybinarysoftware-1.0 mybinarysoftware cd mybinarysoftware less README module load gcc/4.8.2-fasrc01./configure --prefix=$home/apps/mybinarysoftware make make install # add to.bashrc; assumes all binaries are in top level of this folder echo 'export PATH=$HOME/apps/myBinarySoftware:$PATH' >> ~/.bashrc # NB! 's export PATH=$HOME/apps/myBinarySoftware:$PATH # and now run it! mybinary Slide 26

27 Understanding Compiling Code The GNU Build System, also known as the Autotools, is a suite of programming tools designed to assist in making source code packages portable to many Unix- like systems. The GNU Build System makes it possible to build many programs using a two- step process: configure followed by make: module load gcc/4.8.2-fasrc01./configure \ --prefix=$home/apps/mybinarysoftware make make install Slide 27

28 Understanding Compiling Code Slide 28

29 Source Compile Considerations Source Code (.f.f.f95.f03,.c ) main code or driver variables func1on calls subrou1ne Includes / headers (.i or.h) CPATH, C_INCLUDE Libraries files object files (.o) LIBRARY_PATH shared object files (.so) LD_LIBRARY_PATH archive files (.a) sekngs ldconfig LD_LIBRARY_PATH Compilers Intel: ifort, icc, icp, mkl, mpif90,... GNU: gfortran, gcc PGI: pgf90, Abaso: configure scripts make: Makefiles Slide 29

30 Compiling: Configure./configure sets up compile sekngs & target op1ons based on your system environment - - prefix= place to store architecture- independent binaries ($HOME/apps) - - exec- prefix= place to store architecture- dependent binaries - - bindir= where the executables go ( bin/) - - sbindir= system admin executables ( /sbin/) - - includedir= C header files ( include/) - - libdir= object code libraries ( lib/)./configure - - prefix=$home/apps/program./configure - - prefix=$home/apps will have program/bin program/lib etc will have bin/ lib/ include/ etc Some influen1al environment variables: PYTHON python program CXX C++ compiler command CXXFLAGS C++ compiler flags LDFLAGS linker flags if libraries in a nonstd directory <lib dir>: - L$HOME/apps/lib CPPFLAGS C/C++ preprocessor flags if headers in a nonstd directory <include dir>: - I$HOME/apps/include CC C compiler command: gcc CFLAGS C compiler flags: - O3 CXXCPP C++ preprocessor Slide 30

31 Compiling: Make make is a Unix tool to simplify building program executables from many modules. reads in rules (list of target entries) from a user created Makefile run the commands for that given rule will only re- build things that need to be re- built A very simple Makefile all: g++ main.cpp hello.cpp factorial.cpp -o hello install: cp hello $(PREFIX)/bin So make # runs the first (default) command all make install # runs the install rule Influen1al environment variables from previous page affect how the Makefile runs Slide 31

32 Install from Source Code source_tarballs]$ tar xvf tophat tgz source_tarballs]$ ls -al tophat total 1574 drwxr-xr-x 3 bfreeman rc_admin 596 Oct drwxr-xr-x 9 bfreeman rc_admin 1677 Apr 27 17:20.. -rw-r--r-- 1 bfreeman rc_admin Sep aclocal.m4 -rw-r--r-- 1 bfreeman rc_admin 1011 Sep AUTHORS -rw-r--r-- 1 bfreeman rc_admin 7621 Sep ax_boost_base.m4 -rw-r--r-- 1 bfreeman rc_admin 3404 Sep ax_boost_thread.m4 -rw-r--r-- 1 bfreeman rc_admin 0 May ChangeLog -rwxr-xr-x 1 bfreeman rc_admin Sep config.guess -rw-r--r-- 1 bfreeman rc_admin 3079 Sep config.h.in -rwxr-xr-x 1 bfreeman rc_admin Sep config.sub -rwxr-xr-x 1 bfreeman rc_admin Sep configure -rw-r--r-- 1 bfreeman rc_admin 3888 Sep configure.ac -rw-r--r-- 1 bfreeman rc_admin 5206 Sep COPYING -rwxr-xr-x 1 bfreeman rc_admin Sep depcomp -rw-r--r-- 1 bfreeman rc_admin 9478 May INSTALL -rwxr-xr-x 1 bfreeman rc_admin 9233 Sep install-sh -rw-r--r-- 1 bfreeman rc_admin 1469 May LICENSE -rw-r--r-- 1 bfreeman rc_admin 114 Sep Makefile.am -rw-r--r-- 1 bfreeman rc_admin Sep Makefile.in -rwxr-xr-x 1 bfreeman rc_admin Sep missing -rw-r--r-- 1 bfreeman rc_admin 6612 May NEWS -rw-r--r-- 1 bfreeman rc_admin 848 Sep README drwxr-xr-x 4 bfreeman rc_admin 2249 Oct src -rw-r--r-- 1 bfreeman rc_admin 2140 Sep THANKS [bfreeman@sa01 source_tarballs]$ cd!$ # cool trick! last option on prev line [bfreeman@sa01 source_tarballs]$./configure # OPTIONS HERE ARE IMPORTANT INSTALL and README present. Make sure you look thru these! No Makefile here, so have to run./configure Slide 32

33 Compiling: Using Libraries Libraries allow you to pull in pre- compiled func1ons and code to your programs Many are already installed on Odyssey: MKL, NetCDF, LAPACK, etc Should be able to pull in with a simple module load module load beagle/2.1.trunk-fasrc01 But also libraries that may be part of the OS /lib, /lib64 can be pull in via environment variables [bfreeman@sa01 tophat ]$ module display beagle/2.1.trunk-fasrc /n/sw/fasrcsw/modulefiles/core/beagle/2.1.trunk-fasrc03.lua: help([[beagle-2.1.trunk-fasrc03 A general purpose library for evaluating the likelihood of sequence evolution on trees ]], [[ ]]) whatis("name: beagle") whatis("version: 2.1.trunk-fasrc03") whatis("description: A general purpose library for evaluating the likelihood of sequence evolution on trees") prepend_path("cpath","/n/sw/fasrcsw/apps/core/beagle/2.1.trunk-fasrc03/include") prepend_path("fpath","/n/sw/fasrcsw/apps/core/beagle/2.1.trunk-fasrc03/include") prepend_path("ld_library_path","/n/sw/fasrcsw/apps/core/beagle/2.1.trunk-fasrc03/lib") prepend_path("library_path","/n/sw/fasrcsw/apps/core/beagle/2.1.trunk-fasrc03/lib") prepend_path("beagle_path","/n/sw/fasrcsw/apps/core/beagle/2.1.trunk-fasrc03") prepend_path("pkg_config_path","/n/sw/fasrcsw/apps/core/beagle/2.1.trunk-fasrc03/lib/pkgconfig") or -L and -l flags gcc -ltrhead gcc -L/lib64 Slide 33

34 Compiling: CMAKE Tools CMake is an open- source, cross- pla~orm family of tools designed to build, test and package so:ware. CMake is used to control the so:ware compila1on process using simple pla~orm and compiler independent configura1on files, and generate na1ve makefiles and workspaces that can be used in the compiler environment of your choice. Tips: it's best to build out of the so:ware tree (ie mkdir build; cd build; cmake..) -DCMAKE_INSTALL_PREFIX="$HOME/apps/thisapp" -DCMAKE_INCLUDE_PATH:STRING="$BOOST_INCLUDE;$ZLIB_INCLUDE" for include paths -DCMAKE_LIBRARY_PATH:STRING="$BOOST_LIB;$ZLIB_LIB" for lib paths There is a newer version of cmake available as a module seems to be necessary for most these days. module load cmake/ fasrc01 Slide 34

35 Compiling: BOOST Libraries Boost provides free peer- reviewed portable C++ source libraries that work well with the C++ Standard Library. intended to be widely useful usable across a broad spectrum of applica1ons license encourages both commercial and non- commercial use. We aim to establish "exis1ng prac1ce" and provide reference implementa1ons so that Boost libraries are suitable for eventual standardiza1on. Ten Boost libraries are included in the C++ Standards CommiVee's Library Technical Report (TR1) and in the new C++11 Standard. C++11 also includes several more Boost libraries in addi1on to those from TR1. More Boost libraries are proposed for standardiza1on in C++17. FASRC this as a module that is constantly updated: module load boost/ fasrc01 setenv("boost_home","/n/sw/fasrcsw/apps/core/boost/ fasrc01") setenv("boost_include","/n/sw/fasrcsw/apps/core/boost/ fasrc01/include") setenv("boost_lib","/n/sw/fasrcsw/apps/core/boost/ fasrc01/lib") prepend_path("cpath","/n/sw/fasrcsw/apps/core/boost/ fasrc01/include") prepend_path("ld_library_path","/n/sw/fasrcsw/apps/core/boost/ fasrc01/lib") prepend_path("library_path","/n/sw/fasrcsw/apps/core/boost/ fasrc01/lib") If an autotools build does not give you an opportunity to specify non- standard loca1ons for libraries (i.e. there is no - - boost- home or - - boost- lib op1on) can force it by overriding the CC or CXX variable e.g. export CC="gcc -I$BOOST_INCLUDE -L$BOOST_LIB" Slide 35

36 Compiling: Troubleshooting Slide 36

37 Compiling: Take-home Messages Use your.bashrc file to include aliases and environment variables Keep it clean and sparse Organize your home folder as best as possible Use environment variables where possible Pay aven1on to the order of paths in your environment variables Read the README and INSTALL files!! Compiles may go faster on /tmp or /scratch on compute nodes Don't use sudo Watch the compile logs very carefully Be sure to use the module/compiler hierarchy consistently Google is your best friend Next in line is Stack Overflow And then your friendly FASRC person Slide 37

38 Gekng Help RC Website & Documenta1on - - only authorita1ve source hvps://rc.fas.harvard.edu/ Submit a 1cket on the portal hvps://portal.rc.fas.harvard.edu/ Best way to help us to help you? Give us... Descrip1on of problem Addi1onal info (login/batch? par11on? JobIDs?) Steps to Reproduce (1., 2., 3...) Actual results Expected results OdyBot, for quick- fix problems hvp://odybot.org/ 3 8

39 Research Compu1ng Please talk to your peers, and We wish you success in your research! hvp://rc.fas.harvard.edu Harvard 3 9