[0KRunning with gitlab-runner 15.4.0 (43b2dc3d)[0;m [0K on universal-tn4 d3cf9985[0;m section_start:1714596882:prepare_executor [0K[0K[36;1mPreparing the "docker" executor[0;m[0;m [0KUsing Docker executor with image gitlab.kwant-project.org:5005/qt/research-docker ...[0;m [0KAuthenticating with credentials from job payload (GitLab Registry)[0;m [0KPulling docker image gitlab.kwant-project.org:5005/qt/research-docker ...[0;m [0KUsing docker image sha256:fe97fe7a9f41d572be990afbad4d2f2c0bfb33344f892f2d812a915b9a3814d5 for gitlab.kwant-project.org:5005/qt/research-docker with digest gitlab.kwant-project.org:5005/qt/research-docker@sha256:7f1cd32463b6a333d77cea77aaef1b1edf62a9126dde067838e17ef03fe43e2a ...[0;m section_end:1714596891:prepare_executor [0Ksection_start:1714596891:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m Running on runner-d3cf9985-project-3642-concurrent-1 via tnw-tn4.tudelft.net... section_end:1714596896:prepare_script [0Ksection_start:1714596896:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m [32;1mFetching changes with git depth set to 20...[0;m Reinitialized existing Git repository in /builds/qt/kwant-scf/.git/ [32;1mChecking out 92fc4b63 as release_version...[0;m Removing memoryProfile.bin Removing pymf/__pycache__/ Removing pymf/kwant_helper/__pycache__/ Removing pymf/tb/__pycache__/ Removing timeProfile.html [32;1mSkipping Git submodules setup[0;m section_end:1714596901:get_sources [0Ksection_start:1714596901:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m [0KUsing docker image sha256:fe97fe7a9f41d572be990afbad4d2f2c0bfb33344f892f2d812a915b9a3814d5 for gitlab.kwant-project.org:5005/qt/research-docker with digest gitlab.kwant-project.org:5005/qt/research-docker@sha256:7f1cd32463b6a333d77cea77aaef1b1edf62a9126dde067838e17ef03fe43e2a ...[0;m [32;1m$ export PYTHONPATH="."[0;m [32;1m$ pip install memray pyinstrument[0;m WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. Collecting memray Downloading memray-1.12.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB) Collecting pyinstrument Downloading pyinstrument-4.6.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB) Requirement already satisfied: jinja2>=2.9 in /opt/conda/lib/python3.12/site-packages (from memray) (3.1.2) Requirement already satisfied: rich>=11.2.0 in /opt/conda/lib/python3.12/site-packages (from memray) (13.7.1) Collecting textual>=0.41.0 (from memray) Downloading textual-0.58.1-py3-none-any.whl.metadata (5.6 kB) Requirement already satisfied: MarkupSafe>=2.0 in /opt/conda/lib/python3.12/site-packages (from jinja2>=2.9->memray) (2.1.5) Requirement already satisfied: markdown-it-py>=2.2.0 in /opt/conda/lib/python3.12/site-packages (from rich>=11.2.0->memray) (3.0.0) Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /opt/conda/lib/python3.12/site-packages (from rich>=11.2.0->memray) (2.16.1) Requirement already satisfied: typing-extensions<5.0.0,>=4.4.0 in /opt/conda/lib/python3.12/site-packages (from textual>=0.41.0->memray) (4.8.0) Requirement already satisfied: mdurl~=0.1 in /opt/conda/lib/python3.12/site-packages (from markdown-it-py>=2.2.0->rich>=11.2.0->memray) (0.1.2) Collecting linkify-it-py<3,>=1 (from markdown-it-py[linkify,plugins]>=2.1.0->textual>=0.41.0->memray) Downloading linkify_it_py-2.0.3-py3-none-any.whl.metadata (8.5 kB) Requirement already satisfied: mdit-py-plugins in /opt/conda/lib/python3.12/site-packages (from markdown-it-py[linkify,plugins]>=2.1.0->textual>=0.41.0->memray) (0.4.0) Collecting uc-micro-py (from linkify-it-py<3,>=1->markdown-it-py[linkify,plugins]>=2.1.0->textual>=0.41.0->memray) Downloading uc_micro_py-1.0.3-py3-none-any.whl.metadata (2.0 kB) Downloading memray-1.12.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 90.4 MB/s eta 0:00:00 Downloading pyinstrument-4.6.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (106 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 106.5/106.5 kB 192.7 MB/s eta 0:00:00 Downloading textual-0.58.1-py3-none-any.whl (549 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 549.8/549.8 kB 159.2 MB/s eta 0:00:00 Downloading linkify_it_py-2.0.3-py3-none-any.whl (19 kB) Downloading uc_micro_py-1.0.3-py3-none-any.whl (6.2 kB) Installing collected packages: uc-micro-py, pyinstrument, linkify-it-py, textual, memray Successfully installed linkify-it-py-2.0.3 memray-1.12.0 pyinstrument-4.6.2 textual-0.58.1 uc-micro-py-1.0.3 [32;1m$ python profiling/graphene.py[0;m Single SCF loop takes 3.320030429586768 whereas a single diagonalization of a corresponding system takes 1.7600680503994226 [32;1m$ memray stats memoryProfile.bin[0;m 📏 Total allocations: 368585 📦 Total memory allocated: 1.273GB 📊 Histogram of allocation size: min: 8.000B --------------------------------------------- < 47.000B : 358822 ▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇ < 285.000B : 29 ▇ < 1.663KB : 21 ▇ < 9.930KB : 19 ▇ < 59.292KB : 9604 ▇ < 354.032KB: 8 ▇ < 2.064MB : 58 ▇ < 12.326MB : 14 ▇ < 73.599MB : 4 ▇ <=439.453MB: 6 ▇ --------------------------------------------- max: 439.453MB 📂 Allocator type distribution: MALLOC: 368528 MMAP: 55 REALLOC: 2 🥇 Top 5 largest allocating locations (by size): - tb_to_khamvector:/builds/qt/kwant-scf/pymf/tb/transforms.py:40 -> 439.704MB - c2cn:/opt/conda/lib/python3.12/site-packages/scipy/fft/_pocketfft/basic.py:149 -> 264.305MB - density_matrix_kgrid:/builds/qt/kwant-scf/pymf/mf.py:33 -> 175.782MB - ifftn_to_tb:/builds/qt/kwant-scf/pymf/tb/transforms.py:60 -> 105.833MB - eigh:/opt/conda/lib/python3.12/site-packages/numpy/linalg/linalg.py:1487 -> 98.879MB 🥇 Top 5 largest allocating locations (by number of allocations): - ifftn_to_tb:/builds/qt/kwant-scf/pymf/tb/transforms.py:60 -> 358865 - c2cn:/opt/conda/lib/python3.12/site-packages/scipy/fft/_pocketfft/basic.py:149 -> 9627 - eigh:/opt/conda/lib/python3.12/site-packages/numpy/linalg/linalg.py:1487 -> 11 - tb_to_khamvector:/builds/qt/kwant-scf/pymf/tb/transforms.py:34 -> 6 - add_tb:/builds/qt/kwant-scf/pymf/tb/tb.py:19 -> 6 [32;1m$ memray summary memoryProfile.bin[0;m ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━┳━━━━━━━┓ ┃ ┃ ┃ Total ┃ ┃ Own ┃ ┃ ┃ ┃ <Total ┃ Memo… ┃ Own ┃ Memo… ┃ Allo… ┃ ┃ Location ┃ Memor… ┃ % ┃ Memo… ┃ % ┃ Count ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━╇━━━━━━━┩ │ density_matrix at │ 554.9… │ 97.4… │ 0.00… │ 0.00% │ 15 │ │ /builds/qt/kwant-scf/pymf/mf.py │ │ │ │ │ │ │ mfield at │ 554.9… │ 97.4… │ 0.00… │ 0.00% │ 15 │ │ /builds/qt/kwant-scf/pymf/model.py │ │ │ │ │ │ │ scf_loop at │ 554.9… │ 97.4… │ 0.00… │ 0.00% │ 15 │ │ /builds/qt/kwant-scf/profiling/gra… │ │ │ │ │ │ │ <module> at │ 554.9… │ 97.4… │ 0.00… │ 0.00% │ 15 │ │ /builds/qt/kwant-scf/profiling/gra… │ │ │ │ │ │ │ _wrapreduction at │ 88.01… │ 15.4… │ 88.0… │ 15.4… │ 4 │ │ /opt/conda/lib/python3.12/site-pac… │ │ │ │ │ │ │ sum at │ 88.01… │ 15.4… │ 0.00… │ 0.00% │ 4 │ │ /opt/conda/lib/python3.12/site-pac… │ │ │ │ │ │ │ tb_to_khamvector at │ 27.46… │ 4.82% │ 27.4… │ 4.82% │ 2 │ │ /builds/qt/kwant-scf/pymf/tb/trans… │ │ │ │ │ │ │ meshgrid at │ 96.00… │ 0.00% │ 32.0… │ 0.00% │ 3 │ │ /opt/conda/lib/python3.12/site-pac… │ │ │ │ │ │ │ _broadcast_to at │ 64.00… │ 0.00% │ 64.0… │ 0.00% │ 2 │ │ /opt/conda/lib/python3.12/site-pac… │ │ │ │ │ │ │ broadcast_arrays at │ 64.00… │ 0.00% │ 0.00… │ 0.00% │ 2 │ │ /opt/conda/lib/python3.12/site-pac… │ │ │ │ │ │ │ tensordot at │ 32.00… │ 0.00% │ 32.0… │ 0.00% │ 1 │ │ /opt/conda/lib/python3.12/site-pac… │ │ │ │ │ │ └─────────────────────────────────────┴────────┴───────┴───────┴───────┴───────┘ section_end:1714596975:step_script [0Ksection_start:1714596975:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m [32;1mUploading artifacts...[0;m timeProfile.html: found 1 matching files and directories[0;m memoryProfile.bin: found 1 matching files and directories[0;m Uploading artifacts as "archive" to coordinator... 201 Created[0;m id[0;m=420900 responseStatus[0;m=201 Created token[0;m=glcbt-64 section_end:1714596978:upload_artifacts_on_success [0Ksection_start:1714596978:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m section_end:1714596981:cleanup_file_variables [0K[32;1mJob succeeded[0;m