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#71 and #235 progress
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@pavelToman
pavelToman committed Jan 29, 2024
1 parent c20d4a7 commit 5fa6c64
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174 changes: 174 additions & 0 deletions 235_singleM/error_log.txt
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,177 @@
Polars build - problem with Mask bitmask
ERROR:
error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope
--> crates/polars-arrow/src/bitmap/bitmask.rs:152:19
|
152 | Mask::from_bitmask(mask >> byte_shift)
| ^^^^^^^^^^^^ function or associated item not found in `Mask<_, _>`
|
--> crates/polars-arrow/src/bitmap/bitmask.rs:152:19
|
152 | Mask::from_bitmask(mask >> byte_shift)
| ^^^^^^^^^^^^ function or associated item not found in `Mask<_, _>`
|
note: if you're trying to build a new `Mask<_, _>` consider using one of the following associated functions:
Mask::<T, LANES>::splat
Mask::<T, LANES>::from_array
Mask::<T, LANES>::from_int_unchecked
Mask::<T, LANES>::from_int
--> /tmp/vsc47063/easybuild/build/Rust/1.75.0/GCCcore-12.3.0/rustc-1.75.0-src/library/core/src/../../portable-simd/crates/core_simd/src/masks.rs:122:5
= help: items from traits can only be used if the trait is in scope
help: the following trait is implemented but not in scope; perhaps add a `use` for it:
|
1 + use std::simd::ToBitMask;
|
help: there is an associated function with a similar name
|
152 | Mask::from_int(mask >> byte_shift)
| ~~~~~~~~

error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope
--> crates/polars-arrow/src/bitmap/bitmask.rs:159:19
|
159 | Mask::from_bitmask(shifted)
Mask::<T, LANES>::from_int_unchecked
Mask::<T, LANES>::from_int
--> /tmp/vsc47063/easybuild/build/Rust/1.75.0/GCCcore-12.3.0/rustc-1.75.0-src/library/core/src/../../portable-simd/crates/core_simd/src/masks.rs:122:5
= help: items from traits can only be used if the trait is in scope
help: the following trait is implemented but not in scope; perhaps add a `use` for it:
|
1 + use std::simd::ToBitMask;
|
help: there is an associated function with a similar name
|
159 | Mask::from_int(shifted)
| ~~~~~~~~

error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope
--> crates/polars-arrow/src/bitmap/bitmask.rs:161:19
|
161 | Mask::from_bitmask(0u64)
| ^^^^^^^^^^^^ function or associated item not found in `Mask<_, _>`
|
note: if you're trying to build a new `Mask<_, _>` consider using one of the following associated functions:
Mask::<T, LANES>::splat
Mask::<T, LANES>::from_array
Mask::<T, LANES>::from_int_unchecked
Mask::<T, LANES>::from_int
--> /tmp/vsc47063/easybuild/build/Rust/1.75.0/GCCcore-12.3.0/rustc-1.75.0-src/library/core/src/../../portable-simd/crates/core_simd/src/masks.rs:122:5
= help: items from traits can only be used if the trait is in scope
help: the following trait is implemented but not in scope; perhaps add a `use` for it:
|
1 + use std::simd::ToBitMask;
|
help: there is an associated function with a similar name
|
161 | Mask::from_int(0u64)
| ~~~~~~~~

error[E0599]: no function or associated item named `from_bitmask` found for struct `Mask` in the current scope
--> crates/polars-arrow/src/legacy/kernels/agg_mean.rs:95:43
|
95 | let mask = Mask::<i8, LANES>::from_bitmask(validity_chunk as u64);
| ^^^^^^^^^^^^ function or associated item not found in `Mask<i8, 8>`
|
= help: items from traits can only be used if the trait is in scope
help: the following trait is implemented but not in scope; perhaps add a `use` for it:
|
1 + use std::simd::ToBitMask;
|
help: there is an associated function with a similar name
|
95 | let mask = Mask::<i8, LANES>::from_int(validity_chunk as u64);
| ~~~~~~~~

For more information about this error, try `rustc --explain E0599`.
error: could not compile `polars-arrow` (lib) due to 4 previous errors
warning: build failed, waiting for other jobs to finish...
maturin failed
Caused by: Failed to build a native library through cargo
Caused by: Cargo build finished with "exit status: 101": `env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.11-64bit" PYO3_PYTHON="/apps/gent/RHEL8/cascadelake-ib/software/
e-12.3.0/bin/python" PYTHON_SYS_EXECUTABLE="/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python" "cargo" "rustc" "--message-format" "json-render-diagnos
th" "/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/py-polars/Cargo.toml" "--release" "--lib"`
Error: command ['maturin', 'pep517', 'build-wheel', '-i', '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python', '--compatibility', 'off'] returne
us 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for polars
Failed to build polars
ERROR: Could not build wheels for polars, which is required to install pyproject.toml-based projects

####################################################################
Polar build -> problem with cmake:
ERROR:
== 2024-01-22 17:36:52,265 run.py:247 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/geasybuild/RHEL8/cascadelake-ampere-ib/software/polars/0.20.4-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation
. 01-22 17:37:37,595 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in
__init__): cmd " /apelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/so-foss-2023a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output:
Processing /tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: polars
Building wheel for polars (pyproject.toml): started
Building wheel for polars (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error

Building wheel for polars (pyproject.toml) did not run successfully.
exit code: 1
> [230 lines of output]
Running `maturin pep517 build-wheel -i /apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python --compatibility off`
Building a mixed python/rust project
Found pyo3 bindings with abi3 support for Python 3.8
Not using a specific python interpreter
Compiling libc v0.2.151
Compiling proc-macro2 v1.0.74
...
Compiling libz-ng-sys v1.1.12
Compiling xxhash-rust v0.8.8
Compiling itoap v1.0.1
Compiling alloc-no-stdlib v2.0.4
error: failed to run custom build command for `libz-ng-sys v1.1.12`

Caused by:
process didn't exit successfully: `/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/target/release/build/libz-ng-sys-
ld-script-build_zng` (exit status: 101)
--- stdout
CMAKE_TOOLCHAIN_FILE_x86_64-unknown-linux-gnu = None
CMAKE_TOOLCHAIN_FILE_x86_64_unknown_linux_gnu = None
HOST_CMAKE_TOOLCHAIN_FILE = None
CMAKE_TOOLCHAIN_FILE = None
CMAKE_GENERATOR_x86_64-unknown-linux-gnu = None
CMAKE_GENERATOR_x86_64_unknown_linux_gnu = None
HOST_CMAKE_GENERATOR = None
CMAKE_GENERATOR = None
CMAKE_PREFIX_PATH_x86_64-unknown-linux-gnu = None
CMAKE_PREFIX_PATH_x86_64_unknown_linux_gnu = None
HOST_CMAKE_PREFIX_PATH = None
CMAKE_PREFIX_PATH = Some("/apps...)
CMAKE_x86_64-unknown-linux-gnu = None
CMAKE_x86_64_unknown_linux_gnu = None
HOST_CMAKE = None
CMAKE = None
running: cd "/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/target/release/build/libz-ng-sys-659b643918b75119/out/build" && CMAKE_PREFIHEL8/...
--- stderr
thread 'main' panicked at /tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/cmake-0.1.50/src/lib.rs:1098:5:

failed to execute command: No such file or directory (os error 2)
is `cmake` not installed?

build script failed, must exit now
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
warning: build failed, waiting for other jobs to finish...
maturin failed
Caused by: Failed to build a native library through cargo
Caused by: Cargo build finished with "exit status: 101": `env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.11-64bit" PYO3_PYTHON="/apps/gent/R
software/Python/3.11.3-GCCcore-12.3.0/bin/python" PYTHON_SYS_EXECUTABLE="/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/pytho
--message-format" "json-render-diagnostics" "--manifest-path" "/tmp/vsc47063/easybuild/build/polars/0.20.4/foss-2023a/polars/polars-0.20.4/py-polars/Car
"--lib"`
Error: command ['maturin', 'pep517', 'build-wheel', '-i', '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.3-GCCcore-12.3.0/bin/python', '--c
] returned non-zero exit status 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for polars
#############################################################################
Polar build -> bad maturin or cargo?
ERROR:
== 2024-01-18 19:00:19,731 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " /apps/gent/RHftware/Python/3.11.3-GCCcore-12.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/polars/0.20.4s --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output:
Expand Down
26 changes: 18 additions & 8 deletions 235_singleM/polars_cargopython.eb
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
easyblock = "CargoPythonBundle"

name = 'polars'
version = '0.20.4'
version = '0.20.6'

homepage = 'https://pola.rs/'
description = """Lightning-fast DataFrame library for Rust and Python."""
Expand All @@ -10,26 +10,28 @@ toolchain = {'name': 'foss', 'version': '2023a'} #done
toolchainopts = {'pic': True}

builddependencies = [
('Rust', '1.75.0'), #done
('Rust', '1.75.0'),#done
]

dependencies = [
# ('Rust', '1.75.0'),
('Python', '3.11.3'), #done
('Arrow', '14.0.1'), #done
('SciPy-bundle', '2023.07'), #done
('matplotlib', '3.7.2'), #done
('maturin', '1.4.0', '-Rust-1.75.0'), #done
# ('setuptools-rust', '1.6.0'), #done
('poetry', '1.5.1'), #done
('CMake', '3.26.3'), #done
]

# installopts = 'rustup update -- nightly'
prebuildopts = 'rustup update -- nightly && '

exts_list = [
('plot', '0.6.5', {
'checksums': ['453e93798cd21f6a1bfc1fe248237334d6f8a71fea02fd6b9d483476202d1cc2'],
}),
# ('deltalake', '0.15.1', {
# 'checksums': ['77ca8e239297c7db99ae0dd4c13097550f4dca64d6b6f9bd493d9084fdf25fb3'],
# }),
('xlsx2csv', '0.8.2', {
'checksums': ['cdd272c82f8b32f1cee76aeaef87b2ee3549661fddf90f7ecf2310967a16fc84'],
}),
Expand All @@ -38,7 +40,7 @@ exts_list = [
'checksums': ['9403902685b3423cba786db01a36f36efef90ae3d429e45b74dadb4ae9e328dc'],
}),
(name, version, {
'checksums': ['21a90aa0c7401c80fc814b4db371dced780df6bd5ac81a329307e796b5821190'],
'checksums': ['b53553308bc7e2b4f841b18f1949b61ed7f2cf155c5c64712298efa5af67a997'],
}),
]

Expand All @@ -50,6 +52,10 @@ exts_list = [
# 'sanity_pip_check': True,
# 'installopts': '',
# }

# ('deltalake', '0.15.1', {
# 'checksums': ['77ca8e239297c7db99ae0dd4c13097550f4dca64d6b6f9bd493d9084fdf25fb3'],
# }),
# ('setuptools', '65.6.3', {
# 'checksums': ['a7620757bf984b58deaf32fc8a4577a9bbc0850cf92c20e1ce41c38c19e5fb75'],
# }),
Expand Down Expand Up @@ -131,6 +137,8 @@ crates = [
('bincode', '1.3.3'),
('bitflags', '1.3.2'),
('bitflags', '2.4.1'),
# ('bitmap', '3.1.3'),
# ('bitmask', '0.5.0'),
('block-buffer', '0.10.4'),
('brotli', '3.4.0'),
('brotli-decompressor', '2.5.1'),
Expand Down Expand Up @@ -227,7 +235,7 @@ crates = [
('git2', '0.18.1'),
('glob', '0.3.1'),
('group', '0.12.1'),
('h2', '0.3.22'),
('h2', '0.3.24'),
('half', '1.8.2'),
('half', '2.3.1'),
('halfbrown', '0.2.4'),
Expand Down Expand Up @@ -312,7 +320,7 @@ crates = [
('num_cpus', '1.16.0'),
('numpy', '0.20.0'),
('object', '0.32.2'),
('object_store', '0.8.0'),
('object_store', '0.9.0'),
('once_cell', '1.19.0'),
('oorandom', '11.1.3'),
('openssl-probe', '0.1.5'),
Expand Down Expand Up @@ -387,6 +395,8 @@ crates = [
('rustls', '0.21.10'),
('rustls-native-certs', '0.6.3'),
('rustls-pemfile', '1.0.4'),
('rustls-pemfile', '2.0.0'),
('rustls-pki-types', '1.1.0'),
('rustls-webpki', '0.101.7'),
('rustversion', '1.0.14'),
('ryu', '1.0.16'),
Expand Down
12 changes: 8 additions & 4 deletions 71_GRASP_suite/GRASPsuite-2022.7.4-system.eb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,29 +4,33 @@ name = 'GRASP-suite'
version = '2022.7.4'
versionsuffix = '-Java-%(javaver)s'

homepage = 'https://bodenlab.github.io/GRASP-suite/'
homepage = 'https://github.com/bodenlab/GRASP-suite/'

description = """GRASP-suite is a collection of tools and tutorials to perform and
analyse ancestral sequence reconstruction."""

toolchain = SYSTEM

source_urls = ['https://bodenlab.github.io/GRASP-suite/project/graspcmd/archive/']
sources = ['bnkit.jar']
sources = [{
"download_filename": "bnkit.jar",
"filename": "%(name)s-%(version)s.jar",
}]
checksums = ['7ee4cbc9f23857c8c7cf3e6bd0dde962d9a244974d955aac92212b5b5e29a385']

dependencies = [('Java', '17')]

postinstallcmds = [
"mkdir -p %(installdir)s/bin",
"echo '#!/bin/sh' > %(installdir)s/bin/grasp",
"echo 'java -jar -Xmx16g %(installdir)s/bnkit.jar $@' >> %(installdir)s/bin/grasp",
"echo 'java -jar -Xmx16g %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/grasp",
"chmod a+rx %(installdir)s/bin/grasp"
]

sanity_check_commands = ["grasp -h"]

sanity_check_paths = {
'files': ['bin/grasp', 'bnkit.jar'],
'files': ['bin/grasp', '%(name)s-%(version)s.jar'],
'dirs': [],
}

Expand Down

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