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Julia

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Revision as of 15:51, 14 April 2022 by Hpcschlo (talk | contribs)
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The Julia programming language

Julia is a high-productivity, high-performance programming language. It is especially well-suited for numerical computations and scientific computing, with performance on par to traditional statically-compiled languages. At HLRS, the use of Julia is supported on Hawk and Vulcan via the julia module. If you have questions regarding the use of Julia at HLRS, please get in touch with Michael Schlottke-Lakemper.

For users

Getting started

Create SSH SOCKS proxy to install packages

The compute systems at HLRS do not allow internet access from the login nodes. This prevents the out-of-the-box use of Julia’s package manager Pkg.jl, which handles the installation of packages and their dependencies. To enable the use of Pkg.jl again, you need to enable reverse dynamic forwarding when you log in via SSH. This allows Julia to access the internet via your own SSH session. The following instructions (based on this post) work on Unix-like systems with a fairly recent version of OpenSSH (>= 7.6, i.e., post-2017).

Log in to Hawk by executing 

ssh -R SOCKS_PORT hawk.hww.hlrs.de

where SOCKS_PORT should be a five-digit port number from the range of ephemeral port numbers. On Hawk, set the following environment variables to allow Julia to pick up the correct proxy settings when using Pkg.jl: 

export https_proxy=socks5://localhost:SOCKS_PORT
export http_proxy=socks5://localhost:SOCKS_PORT
export JULIA_PKG_USE_CLI_GIT=true # optional

Now, all regular package operations should work as usual. Note: Setting JULIA_PKG_USE_CLI_GIT is optional, as in many cases Pkg.jl will work without it - but it also does not hurt.

To make these changes permanent such that you do not have to execute them manually each time, add the lines above to your startup shell file, e.g., ~/.bash_profile on Hawk. Furthermore, add the following entry to your local ~/.ssh/config file: 

Host hawk.hww.hlrs.de
  RemoteForward SOCKS_PORT

Note that if someone already uses the hardcoded port (even you yourself in a different SSH session), you need to override it by providing the respective SSH arguments on the command line again.

A similar setup for setting up a dynamic reverse proxy also works on Windows when using PuTTY. Instructions (untested) can be found, e.g., here or here (ignore the part about configuring the proxy in Firefox).

Load the Julia module

Right now, just copy-paste the code found below in the Modules setup section below.

TODO: Replace by actual module command.

Note that the Julia module automatically sets your Julia depot path to $HOME/.julia/$SITE_NAME/$SITE_PLATFORM_NAME, where SITE_NAME is HLRS and SITE_PLATFORM_NAME is one of hawk, vulcan, or training. This maintains a separate Julia depot for each system, which makes sense considering that they have different hardware.

Install MPI.jl and CUDA.jl

To install MPI.jl, execute 

julia -e 'using Pkg; Pkg.add("MPI")'

This will download and precompile MPI.jl and all of its dependencies. If you find that the installation produce is stuck at a very early stage (e.g., after outputting only Updating registry at `~/.julia/registries/General.toml`), it means you have not properly set up your SOCKS proxy or forgot to add the appropriate environment variables.

You can check MPI.jl was properly configured by executing 

julia -e 'using MPI; println(MPI.identify_implementation())'

This should give you an output similar to 

(MPI.OpenMPI, v"4.0.5")

If you also want to use the GPUs with Julia, install CUDA.jl by executing 

julia -e 'using Pkg; Pkg.add("CUDA")'

Note that you should not attempt to use or test CUDA.jl on the login nodes, since CUDA is not available here (they do not have GPUs) and thus anything CUDA-related will fail.

Verify that MPI works

Start an interactive session on a compute node by executing 

qsub -I -l select=1:node_type=rome:ncpus=128:mpiprocs=128 -l walltime=00:20:00

Once your interactive job has been allocated, run a simple test program from the shell by executing 

mpirun -np 5 julia mpi_test.jl

The code for mpi_test.jl (based on code found here and here) is as follows: 

# mpi_test.jl
using MPI

MPI.Init()
comm = MPI.COMM_WORLD
rank = MPI.Comm_rank(comm)
size = MPI.Comm_size(comm)

dst = mod(rank+1, size)
src = mod(rank-1, size)
println("rank=$rank, size=$size, dst=$dst, src=$src")

# allocate memory
N = 4
send_mesg = Array{Float64}(undef, N)
recv_mesg = Array{Float64}(undef, N)
fill!(send_mesg, Float64(rank))

# pass buffers into MPI functions
MPI.Sendrecv!(send_mesg, dst, 0, recv_mesg, src, 0, comm)
println("recv_mesg on proc $rank: $recv_mesg")

If everything is working OK, it should give you an output similar to 

rank=0, size=5, dst=1, src=4
rank=1, size=5, dst=2, src=0
rank=2, size=5, dst=3, src=1
rank=3, size=5, dst=4, src=2
rank=4, size=5, dst=0, src=3
recv_mesg on proc 2: [1.0, 1.0, 1.0, 1.0]
recv_mesg on proc 1: [0.0, 0.0, 0.0, 0.0]
recv_mesg on proc 3: [2.0, 2.0, 2.0, 2.0]
recv_mesg on proc 0: [4.0, 4.0, 4.0, 4.0]
recv_mesg on proc 4: [3.0, 3.0, 3.0, 3.0]

Verify that CUDA works

To test CUDA, you need to leave your interactive session on a CPU node and get an interactive session on a GPU node by running 

qsub -I -l select=1:node_type=nv-a100-40gb:mpiprocs=8 -l walltime=00:20:00

The first test is to check whether CUDA.jl can find all relevant drivers and GPUs. Start the Julia REPL by running julia. Then, execute 

julia> using CUDA

julia> CUDA.versioninfo()
CUDA toolkit 11.4, local installation
NVIDIA driver 470.57.2, for CUDA 11.4
CUDA driver 11.4

Libraries:
- CUBLAS: 11.5.4
- CURAND: 10.2.5
- CUFFT: 10.5.1
- CUSOLVER: 11.2.0
- CUSPARSE: 11.6.0
- CUPTI: 14.0.0
- NVML: 11.0.0+470.57.2
- CUDNN: missing
- CUTENSOR: missing

Toolchain:
- Julia: 1.7.2
- LLVM: 12.0.1
- PTX ISA support: 3.2, 4.0, 4.1, 4.2, 4.3, 5.0, 6.0, 6.1, 6.3, 6.4, 6.5, 7.0
- Device capability support: sm_35, sm_37, sm_50, sm_52, sm_53, sm_60, sm_61, sm_62, sm_70, sm_72, sm_75, sm_80

Environment:
- JULIA_CUDA_USE_MEMORY_POOL: none
- JULIA_CUDA_USE_BINARYBUILDER: false

8 devices:
  0: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  1: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  2: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  3: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  4: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  5: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  6: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)
  7: NVIDIA A100-SXM4-40GB (sm_80, 39.583 GiB / 39.586 GiB available)

As you can see, all 8 Nvidia Tesla A100 GPUs have been correctly detected.

Next, we will test if computing on the GPU is actually faster than on the CPU, to ensure that actual computations work. For this, paste the following snippet (based on code found here) in the Julia REPL. Approximate timings are included as reference for you: 

A = rand(2000, 2000);
B = rand(2000, 2000);
@time A*B; # 1.296624 seconds (2.52 M allocations: 155.839 MiB, 23.66% gc time, 65.33% compilation time)
@time A*B; # 0.341631 seconds (2 allocations: 30.518 MiB)

Agpu = CuArray(A); # move matrix to gpu
Bgpu = CuArray(B); # move matrix to gpu
@time Agpu*Bgpu; # 1.544657 seconds (1.54 M allocations: 81.926 MiB, 2.16% gc time, 59.89% compilation time)
@time Agpu*Bgpu; # 0.000627 seconds (32 allocations: 640 bytes)

As you can see, the matrix-matrix multiplication on the GPU is much faster than on the CPU.

Where to go from here?

With the above steps completed, you are ready to run Julia-based programs in parallel on Hawk! With the initial setup completed, in future sessions you only need to load the appropriate Julia module with module load julia and everything else should be set up for you.

For admins

Module setup

It would be great if we could have a julia/1.7.2 namespacing to support different Julia versions, where the default should be the latest stable version. Based on the original Julia module file for testing, provided by AR in November 2021, the Julia module file could look something like the following: 

#%Module1.0
#
# =============================================================================
# Installation info :
#
# =============================================================================

set VERSION "1.7.2"
set PREFIX  "/lustre/hpe/ws10/ws10.3/ws/hpcaruop-ws10test02/hawk/julia/installation"
set BASEDIR "${PREFIX}/${VERSION}"
set CAT     "julia"

# do _not_ set GCC_ROOT as this is internally used by GCC and hence triggers
# undesired behavior!
setenv JULIA_HOME    ${BASEDIR}
setenv JULIA_VERSION ${VERSION}

set MODULE_TEXT        "Julia"
set HELPTEXT           "${MODULE_TEXT}\nversion ${VERSION}"
set EXTERNAL_REFERENCE "https://julialang.org/"
set DESCRIPTION        "Julia is a high-productivity, high-performance programming language, and is especially well-suited for scientific computing and data analysis."

conflict ${CAT}
depends_on openmpi

prepend-path PATH               ${BASEDIR}/bin
prepend-path LD_LIBRARY_PATH    ${BASEDIR}/lib
prepend-path MANPATH            ${BASEDIR}/share/man
prepend-path CPATH              ${BASEDIR}/include

# Julia-related settings
setenv       JULIA_DEPOT_PATH   "$HOME/.julia/$SITE_NAME/$SITE_PLATFORM_NAME"

# MPI-related settings
setenv       JULIA_MPI_BINARY   system

# CUDA-related settings
setenv       JULIA_CUDA_USE_BINARYBUILDER false
setenv       JULIA_CUDA_USE_MEMORY_POOL   none
# CUDA_PATH is only relevant on AI nodes but always set anyways
setenv       CUDA_PATH                    /usr/local/cuda

# Other settings
# suppress UCX warnings
setenv       UCX_WARN_UNUSED_ENV_VARS     n

module-whatis "Julia version $VERSION: ${DESCRIPTION}."

proc ModulesHelp {} {
	global MODULE_TEXT
	global VERSION
	global EXTERNAL_REFERENCE
        puts stderr "${DESCRIPTION}"
        puts stderr ""
	puts stderr "This module sets up the environment for $MODULE_TEXT by adding"
	puts stderr "corresponding values to PATH, LD_LIBRARY_PATH and MANPATH."
	puts stderr "Module:         ${MODULE}"
	puts stderr "Version:        ${VERSION}"
	puts stderr "For further information visit"
	puts stderr "> ${EXTERNAL_REFERENCE}"
}

# prohibit loading multiple compilers (Lmod-specific feature)
# family compiler


Until the module file is available, just execute the following commands in your shell: 

# Julia-related settings
export JULIA_DEPOT_PATH="$HOME/.julia/$SITE_NAME/$SITE_PLATFORM_NAME"

# MPI-related settings
module load openmpi
export JULIA_MPI_BINARY=system

# CUDA-related settings
export CUDA_PATH=/usr/local/cuda
export JULIA_CUDA_USE_BINARYBUILDER=false
export JULIA_CUDA_USE_MEMORY_POOL=none

# Other settings
export UCX_WARN_UNUSED_ENV_VARS=n # suppress UCX warnings

MPT not working with Julia

Right now there seems to be an issue with using HPE's MPT as the MPI backend in MPI.jl, resulting in abort when trying to run even a simple MPI program on one rank (see also https://github.com/JuliaLang/julia/issues/44969). It would be great if this can be fixed. In the meantime, we can use OpenMPI (see module code above).

CUDA-aware MPI

At the moment, OpenMPI does not seem to support CUDA-aware MPI on the Hawk AI nodes. Instead, the execution crashes with a segmentation fault. To reproduce, log in to one of the AI nodes and execute 

mpirun -np 5 julia cuda_mpi_test.jl

where cuda_mpi_test.jl is given as follows: 

# cuda_mpi_test.jl
using MPI
using CUDA

MPI.Init()
comm = MPI.COMM_WORLD
rank = MPI.Comm_rank(comm)
size = MPI.Comm_size(comm)

dst = mod(rank+1, size)
src = mod(rank-1, size)
println("rank=$rank, size=$size, dst=$dst, src=$src")

# allocate memory on the GPU
N = 4
send_mesg = CuArray{Float64}(undef, N)
recv_mesg = CuArray{Float64}(undef, N)
fill!(send_mesg, Float64(rank))

# pass GPU buffers (CuArrays) into MPI functions
MPI.Sendrecv!(send_mesg, dst, 0, recv_mesg, src, 0, comm)
println("recv_mesg on proc $rank: $recv_mesg")

This will crash with an error similar to this: 

rank=4, size=5, dst=0, src=3
rank=0, size=5, dst=1, src=4
rank=2, size=5, dst=3, src=1
rank=1, size=5, dst=2, src=0
rank=3, size=5, dst=4, src=2
[hawk-ai01:263609:0:263609] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0xa02000000)
[hawk-ai01:263605:0:263605] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0xa02000000)
[hawk-ai01:263607:0:263607] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0xa02000000)
[hawk-ai01:263606:0:263606] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0xa02000000)
[hawk-ai01:263608:0:263608] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0xa02000000)
==== backtrace (tid: 263606) ====
 0 0x00000000000532f9 ucs_debug_print_backtrace()  ???:0
 1 0x0000000000012b20 .annobin_sigaction.c()  sigaction.c:0
 2 0x000000000015dd3b __memcpy_avx_unaligned()  :0
 3 0x0000000000043f4f ucp_wireup_select_sockaddr_transport()  ???:0
 4 0x00000000000148c9 uct_mm_ep_am_bcopy()  ???:0
 5 0x0000000000043fcb ucp_wireup_select_sockaddr_transport()  ???:0
 6 0x000000000003a74a ucp_tag_send_nbr()  ???:0
 7 0x00000000001c7e4f mca_pml_ucx_send()  ???:0
 8 0x00000000000bba69 PMPI_Sendrecv()  ???:0
 9 0x00000000000c4e0a _jl_invoke()  /buildworker/worker/package_linux64/build/src/gf.c:2247
10 0x00000000000e3e96 jl_apply()  /buildworker/worker/package_linux64/build/src/julia.h:1788
11 0x00000000000e390e eval_value()  /buildworker/worker/package_linux64/build/src/interpreter.c:215
12 0x00000000000e46d2 eval_stmt_value()  /buildworker/worker/package_linux64/build/src/interpreter.c:166
13 0x00000000000e46d2 eval_stmt_value()  /buildworker/worker/package_linux64/build/src/interpreter.c:167
14 0x00000000000e46d2 eval_body()  /buildworker/worker/package_linux64/build/src/interpreter.c:587
15 0x00000000000e52f8 jl_interpret_toplevel_thunk()  /buildworker/worker/package_linux64/build/src/interpreter.c:731
16 0x00000000001027a4 jl_toplevel_eval_flex()  /buildworker/worker/package_linux64/build/src/toplevel.c:885
17 0x00000000001029e5 jl_toplevel_eval_flex()  /buildworker/worker/package_linux64/build/src/toplevel.c:830
18 0x000000000010462a jl_toplevel_eval_in()  /buildworker/worker/package_linux64/build/src/toplevel.c:944
19 0x000000000115a83b eval()  ./boot.jl:373
20 0x000000000115a83b japi1_include_string_40536()  ./loading.jl:1196
21 0x00000000000c4e0a _jl_invoke()  /buildworker/worker/package_linux64/build/src/gf.c:2247
22 0x000000000124a35b japi1__include_32082()  ./loading.jl:1253
23 0x0000000000d67c16 japi1_include_36299()  ./Base.jl:418
24 0x00000000000c4e0a _jl_invoke()  /buildworker/worker/package_linux64/build/src/gf.c:2247
25 0x00000000012d064c julia_exec_options_33549()  ./client.jl:292
26 0x0000000000d8a0f8 julia__start_38731()  ./client.jl:495
27 0x0000000000d8a269 jfptr__start_38732.clone_1()  text:0
28 0x00000000000c4e0a _jl_invoke()  /buildworker/worker/package_linux64/build/src/gf.c:2247
29 0x00000000001282d6 jl_apply()  /buildworker/worker/package_linux64/build/src/julia.h:1788
30 0x0000000000128c7d jl_repl_entrypoint()  /buildworker/worker/package_linux64/build/src/jlapi.c:701
31 0x00000000004007d9 main()  /buildworker/worker/package_linux64/build/cli/loader_exe.c:42
32 0x00000000000237b3 __libc_start_main()  ???:0
33 0x0000000000400809 _start()  ???:0
=================================

signal (11): Segmentation fault
in expression starting at /zhome/academic/HLRS/hlrs/hpcschlo/cuda_mpi_test.jl:21
__memmove_avx_unaligned at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x147c167e3f4e)
uct_mm_ep_am_bcopy at /lib64/libuct.so.0 (unknown line)
unknown function (ip: 0x147c167e3fca)
ucp_tag_send_nbr at /lib64/libucp.so.0 (unknown line)
mca_pml_ucx_send at /opt/hlrs/non-spack/mpi/openmpi/4.0.5-gcc-9.2.0/lib/libmpi.so (unknown line)
PMPI_Sendrecv at /opt/hlrs/non-spack/mpi/openmpi/4.0.5-gcc-9.2.0/lib/libmpi.so (unknown line)
Sendrecv! at /zhome/academic/HLRS/hlrs/hpcschlo/.julia/HLRS/hawk/packages/MPI/08SPr/src/pointtopoint.jl:380 [inlined]
Sendrecv! at /zhome/academic/HLRS/hlrs/hpcschlo/.julia/HLRS/hawk/packages/MPI/08SPr/src/pointtopoint.jl:389
unknown function (ip: 0x147c1a1062fb)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:126
[...]
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