Comments (3)
tgy
commented on June 10, 2024
1
thanks @dantegd :)
Click here to see environment details
**git*** Not inside a git repository ***OS Information*** NAME="Rocky Linux" VERSION="9.3 (Blue Onyx)" ID="rocky" ID_LIKE="rhel centos fedora" VERSION_ID="9.3" PLATFORM_ID="platform:el9" PRETTY_NAME="Rocky Linux 9.3 (Blue Onyx)" ANSI_COLOR="0;32" LOGO="fedora-logo-icon" CPE_NAME="cpe:/o:rocky:rocky:9::baseos" HOME_URL="https://rockylinux.org/" BUG_REPORT_URL="https://bugs.rockylinux.org/" SUPPORT_END="2032-05-31" ROCKY_SUPPORT_PRODUCT="Rocky-Linux-9" ROCKY_SUPPORT_PRODUCT_VERSION="9.3" REDHAT_SUPPORT_PRODUCT="Rocky Linux" REDHAT_SUPPORT_PRODUCT_VERSION="9.3" Rocky Linux release 9.3 (Blue Onyx) Rocky Linux release 9.3 (Blue Onyx) Rocky Linux release 9.3 (Blue Onyx) Linux 5.14.0-362.8.1.el9_3.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Nov 8 17:36:32 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux ***GPU Information*** Fri Dec 8 18:25:28 2023 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.129.03 Driver Version: 535.129.03 CUDA Version: 12.2 | |-----------------------------------------+----------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+======================+======================| | 0 NVIDIA GeForce RTX 4090 Off | 00000000:0A:00.0 Off | Off | | 31% 53C P0 58W / 450W | 2MiB / 24564MiB | 0% Default | | | | N/A | +-----------------------------------------+----------------------+----------------------+ | 1 NVIDIA GeForce RTX 4090 Off | 00000000:0B:00.0 Off | Off | | 30% 41C P0 N/A / 450W | 2MiB / 24564MiB | 0% Default | | | | N/A | +-----------------------------------------+----------------------+----------------------+ +---------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=======================================================================================| | No running processes found | +---------------------------------------------------------------------------------------+ ***CPU*** Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 48 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 24 On-line CPU(s) list: 0-23 Vendor ID: AuthenticAMD Model name: AMD Ryzen 9 5900X 12-Core Processor CPU family: 25 Model: 33 Thread(s) per core: 2 Core(s) per socket: 12 Socket(s): 1 Stepping: 2 Frequency boost: enabled CPU max MHz: 3700.0000 CPU min MHz: 2200.0000 BogoMIPS: 7400.40 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf rapl pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate ssbd mba ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl umip pku ospke vaes vpclmulqdq rdpid overflow_recov succor smca fsrm Virtualization: AMD-V L1d cache: 384 KiB (12 instances) L1i cache: 384 KiB (12 instances) L2 cache: 6 MiB (12 instances) L3 cache: 64 MiB (2 instances) NUMA node(s): 1 NUMA node0 CPU(s): 0-23 Vulnerability Gather data sampling: Not affected Vulnerability Itlb multihit: Not affected Vulnerability L1tf: Not affected Vulnerability Mds: Not affected Vulnerability Meltdown: Not affected Vulnerability Mmio stale data: Not affected Vulnerability Retbleed: Not affected Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Retpolines, IBPB conditional, IBRS_FW, STIBP always-on, RSB filling, PBRSB-eIBRS Not affected Vulnerability Srbds: Not affected Vulnerability Tsx async abort: Not affected ***CMake*** /usr/bin/cmake cmake version 3.20.2 CMake suite maintained and supported by Kitware (kitware.com/cmake). ***g++*** /usr/bin/g++ g++ (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2) Copyright (C) 2021 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ***nvcc*** /home/v/miniforge3/envs/rapids/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Mon_Oct_24_19:12:58_PDT_2022 Cuda compilation tools, release 12.0, V12.0.76 Build cuda_12.0.r12.0/compiler.31968024_0 ***Python*** /home/v/miniforge3/envs/rapids/bin/python Python 3.10.13 ***Environment Variables*** PATH : /home/v/miniforge3/envs/rapids/bin:/home/v/miniforge3/condabin:/home/v/.local/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/v/bin LD_LIBRARY_PATH : NUMBAPRO_NVVM : NUMBAPRO_LIBDEVICE : CONDA_PREFIX : /home/v/miniforge3/envs/rapids PYTHON_PATH : ***conda packages*** /home/v/miniforge3/condabin/conda # packages in environment at /home/v/miniforge3/envs/rapids: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge aiohttp 3.9.1 py310h2372a71_0 conda-forge aiosignal 1.3.1 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libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libsystemd0 254 h3516f8a_0 conda-forge libtasn1 4.19.0 h166bdaf_0 conda-forge libtheora 1.1.1 h7f98852_1005 conda-forge libthrift 0.19.0 hb90f79a_1 conda-forge libtiff 4.6.0 ha9c0a0a_2 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.46.0 hd590300_0 conda-forge libva 2.20.0 hd590300_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libvpx 1.13.1 h59595ed_0 conda-forge libwebp 1.3.2 h658648e_1 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxgboost 1.7.6 rapidsai_hfb38c85_2310 rapidsai libxkbcommon 1.6.0 h5d7e998_0 conda-forge libxml2 2.11.6 h232c23b_0 conda-forge libxslt 1.1.37 h0054252_1 conda-forge libzip 1.10.1 h2629f0a_3 conda-forge libzlib 1.2.13 hd590300_5 conda-forge libzopfli 1.0.3 h9c3ff4c_0 conda-forge linkify-it-py 2.0.0 pyhd8ed1ab_0 conda-forge llvm-openmp 17.0.6 h4dfa4b3_0 conda-forge llvmlite 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conda-forge pulseaudio-client 16.1 hb77b528_5 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge py-xgboost 1.7.6 rapidsai_py310h1395376_2310 rapidsai pyarrow 12.0.1 py310hf9e7431_14_cpu conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyct 0.5.0 pyhd8ed1ab_0 conda-forge pyee 8.1.0 pyhd8ed1ab_0 conda-forge pygments 2.17.2 pyhd8ed1ab_0 conda-forge pylibcugraph 23.10.00 cuda12_py310_231011_gc3dc860d_0 rapidsai pylibraft 23.10.00 cuda12_py310_231011_gafdddfb3_0 rapidsai pymatreader 0.0.32 pyhd8ed1ab_0 conda-forge pynvml 11.4.1 pyhd8ed1ab_0 conda-forge pyodbc 5.0.1 py310hc6cd4ac_0 conda-forge pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pyppeteer 1.0.2 pyhd8ed1ab_0 conda-forge pyproj 3.6.1 py310h32c33b7_4 conda-forge pyqt 5.15.9 py310h04931ad_5 conda-forge pyqt5-sip 12.12.2 py310hc6cd4ac_5 conda-forge pyqtgraph 0.13.3 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.9.2 py310h374b01c_0 conda-forge pytest 7.4.3 pyhd8ed1ab_0 conda-forge python 3.10.13 hd12c33a_0_cpython conda-forge python-confluent-kafka 1.9.2 py310h5764c6d_2 conda-forge python-daemon 3.0.1 pyhd8ed1ab_2 conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-picard 0.7 pyh8a188c0_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytorch 2.0.0 cpu_mkl_py310h44e7ea7_102 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyvista 0.42.3 pyhd8ed1ab_0 conda-forge pyvistaqt 0.11.0 pyhd8ed1ab_1 conda-forge pyviz_comms 3.0.0 pyhd8ed1ab_0 conda-forge pywavelets 1.4.1 py310h1f7b6fc_1 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge pyzmq 25.1.1 py310h795f18f_2 conda-forge qdarkstyle 3.2 pyhd8ed1ab_0 conda-forge qt-main 5.15.8 h82b777d_17 conda-forge qtconsole-base 5.5.1 pyha770c72_0 conda-forge qtpy 2.4.1 pyhd8ed1ab_0 conda-forge raft-dask 23.10.00 cuda12_py310_231011_gafdddfb3_0 rapidsai rapids 23.10.00 cuda12_py310_231011_gd3958fe_0 rapidsai rapids-xgboost 23.10.00 cuda12_py310_231011_gd3958fe_0 rapidsai rav1e 0.6.6 he8a937b_2 conda-forge rdma-core 28.9 h59595ed_1 conda-forge re2 2023.03.02 h8c504da_0 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.31.1 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rich 13.7.0 pyhd8ed1ab_0 conda-forge rmm 23.10.00 cuda12_py310_231011_gf8ac6f8e_0 rapidsai rpds-py 0.13.2 py310hcb5633a_0 conda-forge rtree 1.1.0 py310hbdcdc62_0 conda-forge s2n 1.3.54 h06160fa_0 conda-forge scikit-image 0.21.0 py310hc6cd4ac_0 conda-forge scikit-learn 1.3.2 py310h1fdf081_1 conda-forge scipy 1.11.4 py310hb13e2d6_0 conda-forge scooby 0.9.2 pyhd8ed1ab_0 conda-forge seaborn 0.13.0 hd8ed1ab_0 conda-forge seaborn-base 0.13.0 pyhd8ed1ab_0 conda-forge send2trash 1.8.2 pyh41d4057_0 conda-forge setuptools 68.2.2 pyhd8ed1ab_0 conda-forge shapely 2.0.2 py310hc3e127f_1 conda-forge simpervisor 1.0.0 pyhd8ed1ab_0 conda-forge sip 6.7.12 py310hc6cd4ac_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge skorch 0.15.0 pyh7448d05_0 conda-forge sleef 3.5.1 h9b69904_2 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge spdlog 1.11.0 h9b3ece8_1 conda-forge sqlalchemy 2.0.23 py310h2372a71_0 conda-forge sqlite 3.44.2 h2c6b66d_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge statsmodels 0.14.0 py310h1f7b6fc_2 conda-forge streamz 0.6.4 pyh6c4a22f_0 conda-forge svt-av1 1.7.0 h59595ed_0 conda-forge sympy 1.12 pypyh9d50eac_103 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge tbb 2021.10.0 h00ab1b0_2 conda-forge tbb-devel 2021.10.0 h00ab1b0_2 conda-forge tblib 2.0.0 pyhd8ed1ab_0 conda-forge tenacity 8.2.3 pyhd8ed1ab_0 conda-forge terminado 0.18.0 pyh0d859eb_0 conda-forge threadpoolctl 3.2.0 pyha21a80b_0 conda-forge tifffile 2023.9.26 pyhd8ed1ab_0 conda-forge tiledb 2.16.3 h8c794c1_3 conda-forge tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.3.3 py310h2372a71_1 conda-forge tqdm 4.66.1 pyhd8ed1ab_0 conda-forge traitlets 5.14.0 pyhd8ed1ab_0 conda-forge trame 3.3.0 pyhd8ed1ab_0 conda-forge trame-client 2.13.0 pyhd8ed1ab_0 conda-forge trame-components 2.2.1 pyhd8ed1ab_0 conda-forge trame-deckgl 2.0.2 pyhd8ed1ab_0 conda-forge trame-markdown 2.0.2 pyhd8ed1ab_0 conda-forge trame-matplotlib 2.0.2 pyhd8ed1ab_0 conda-forge trame-plotly 2.1.1 pyhd8ed1ab_0 conda-forge trame-rca 0.4.1 pyhd8ed1ab_0 conda-forge trame-router 2.1.0 pyhd8ed1ab_0 conda-forge trame-server 2.12.1 pyhd8ed1ab_0 conda-forge trame-simput 2.3.3 pyhd8ed1ab_0 conda-forge trame-vega 2.0.3 pyhd8ed1ab_0 conda-forge trame-vtk 2.6.2 pyhd8ed1ab_0 conda-forge trame-vuetify 2.3.1 pyhd8ed1ab_0 conda-forge treelite 3.9.1 py310h4a6579d_0 conda-forge treelite-runtime 3.9.1 pypi_0 pypi types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge typing-extensions 4.8.0 hd8ed1ab_0 conda-forge typing_extensions 4.8.0 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge tzcode 2023c h0b41bf4_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge uc-micro-py 1.0.1 pyhd8ed1ab_0 conda-forge ucx 1.14.1 h195a15c_5 conda-forge ucx-proc 1.0.0 gpu rapidsai ucx-py 0.34.00 py310_231011_g17dceab_0 rapidsai unicodedata2 15.1.0 py310h2372a71_0 conda-forge unixodbc 2.3.12 h661eb56_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge uriparser 0.9.7 hcb278e6_1 conda-forge urllib3 1.26.18 pyhd8ed1ab_0 conda-forge utfcpp 4.0.1 ha770c72_0 conda-forge vtk 9.2.6 qt_py310h1234567_219 conda-forge vtk-base 9.2.6 qt_py310h1234567_219 conda-forge vtk-io-ffmpeg 9.2.6 qt_py310h1234567_219 conda-forge wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge webcolors 1.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge websockets 10.4 py310h5764c6d_1 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge wrapt 1.16.0 py310h2372a71_0 conda-forge wslink 1.12.4 pyhd8ed1ab_0 conda-forge x264 1!164.3095 h166bdaf_2 conda-forge x265 3.5 h924138e_3 conda-forge xarray 2023.11.0 pyhd8ed1ab_0 conda-forge xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xerces-c 3.2.4 hac6953d_3 conda-forge xgboost 1.7.6 rapidsai_py310h1395376_2310 rapidsai xkeyboard-config 2.40 hd590300_0 conda-forge xlrd 2.0.1 pyhd8ed1ab_3 conda-forge xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xyzservices 2023.10.1 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.9.3 py310h2372a71_0 conda-forge zeromq 4.3.5 h59595ed_0 conda-forge zfp 1.0.0 h59595ed_4 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forgenote that i managed to run the training with
n_neighbors <= 200, it's when I increased the value ofn_neighborsto256or more that the memory blew upinstead of a bug, this could simply be due to the memory usage required to handle a high number of neighbors? i have no idea what hyperparams of UMAP can cause it to consume too much memory
note that i've tried using the
umap-learnPython library and the memory blew up as well withn_neighbors = 256i think it would be worth it to explain the effect of certain values of the hyperparameters on the memory and time requirements of algorithm
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dantegd commented on June 10, 2024
Thanks for the issue @tgy! This might be related to #5690, or maybe not, but could I ask if you could run the script https://github.com/rapidsai/cuml/blob/branch-24.02/print_env.sh and paste the output in this issue? That'll help us triage and see the versions of everything in your environment.
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alisiahkoohi commented on June 10, 2024
I also have similar hyper-parameters but I have additional concerns. I run into memory issues when calling UMAP
fit_transform()in a for loop for different datasets as a result of growing GPU usage. The script looks like the followingumap_features = [] for i in range(len(dataset)): umap_features.append(UMAP( n_neighbors=300, min_dist=5e-1, metric='euclidean', verbose=True, ).fit_transform(dataset[i]))Is there any built-in function for clearing out GPU memory?
Edit: Just saw this: #5666.
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Related Issues (20)
- [DOC] ImportError: cannot import name 'make_column_transformer' from 'cuml.preprocessing'
- [BUG] OneHotEncoder doesn't work in neither string nor numeric columns
- [FEA] Support `feature_names_in_` attribute
- [BUG] Failed to execute HalvingRandomSearchCV: It is very likely that your model is misconfigured HOT 1
- [BUG] Transient illegal memory access when performing umap.transform() HOT 2
- [BUG] **`_process_generic` defined in `base_helpers` but needed in `base_return_types`, circular import restricted** HOT 2
- [QST] I am not able to find feature selection methods in cuML. HOT 1
- [BUG] Pipeline of MinMaxScaler and KMeans with DataFrame input produces incorrect results
- [FEA] nan_euclidean or custom metric added as a metric in NearestNeighbors HOT 2
- [BUG] the UMAP implementation much worse than on CPU HOT 1
- [FEA] Custom initial embedding for UMAP
- [BUG] CountVectorizer Vocabulary Length Mismatch HOT 2
- [FEA] Unified Interface for Model Interpretability in cuML HOT 1
- [QST] Is it OK to mix Ampere & Ada Lovelace cards when distributing workload
- [FEA] Cuml for windows! When?!
- [BUG] Using precomputed KNN with more neighbors than `n_neighbors` drops trustworthiness score for UMAP
- [BUG] HDBSCAN condensed tree and single linkage raise errors HOT 1
- [BUG] A warning (Warning: could not fill working set) poped up when fitting svm.SVC
- GridSearchCV GPU Implemetation
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