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Anurag1734/cuda-error-resolution-analysis

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I tried to interconnect all the nodes to start, but for some reason PyTorch Geometric doesn’t like my edge index matrix.</p>\n<p>I am getting the following error:</p>\n<p>ValueError: <code>MessagePassing.propagate</code> only supports integer tensors of shape <code>[2, num_messages]</code>, <code>torch_sparse.SparseTensor</code> or <code>torch.sparse.Tensor</code> for argument <code>edge_index</code>.</p>\n<p>What am I doing wrong?</p>\n<pre><code class=\"lang-auto\">def make_edge_index(node_size):\n    rows = []\n    columns = []\n    for i in range(node_size):\n        for j in range(node_size):\n            rows.append(i)\n            columns.append(j)\n    rows = np.asarray(rows)\n    columns = np.asarray(columns)\n    index = np.zeros(shape=(2, node_size*node_size))\n    index[0,:] = rows\n    index[1,:] = columns\n    return index\n\nself.input_size = int(node_size/2)\nself.output_size = 4\nself.edge_matrix = make_edge_index(self.input_size)\nself.GCN = geom_nn.conv.GCNConv(2, self.output_size)\nself.linear_layer = nn.Linear(node_size, self.input_size)\n\n\nx = torch.swapaxes(x, 1, 2)\nx = x.float()\nx = self.linear_layer(x)\n# start by scaling down all possible hits using input layer\nx = torch.swapaxes(x, 1, 2)\nx = self.GCN(x, self.edge_matrix)\n\n</code></pre>",12          "post_number": 1,13          "post_type": 1,14          "posts_count": 1,15          "updated_at": "2024-02-16T00:50:03.621Z",16          "reply_count": 0,17          "reply_to_post_number": null,18          "quote_count": 0,19          "incoming_link_count": 196,20          "reads": 6,21          "readers_count": 5,22          "score": 981.2,23          "yours": false,24          "topic_id": 197162,25          "topic_slug": "graph-convolutional-neural-network-issues",26          "display_username": "Cwoolfo1",27          "primary_group_name": null,28          "flair_name": null,29          "flair_url": null,30          "flair_bg_color": null,31          "flair_color": null,32          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I am training a model using DDP on AWS Sagemaker. I am using a single instance with multiple GPUs. There is a large dataset on S3 and it seems I need to download the data on each of the ranks. The data is downloaded and then a dataset/data loader is created. If data is downloaded - read into memory via pandas - does that mean that the GPU memory is being used to read in the data into pandas since it needs to happen on each rank?</p>",463          "post_number": 1,464          "post_type": 1,465          "posts_count": 8,466          "updated_at": "2024-02-15T03:52:15.182Z",467          "reply_count": 0,468          "reply_to_post_number": null,469          "quote_count": 0,470          "incoming_link_count": 122,471          "reads": 10,472          "readers_count": 9,473          "score": 597.0,474          "yours": false,475          "topic_id": 197125,476          "topic_slug": "what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus",477          "display_username": "PopHSKE",478          "primary_group_name": null,479          "flair_name": null,480          "flair_url": null,481          "flair_bg_color": null,482          "flair_color": null,483          "flair_group_id": null,484          "badges_granted": [],485          "version": 1,486          "can_edit": false,487          "can_delete": false,488          "can_recover": false,489          "can_see_hidden_post": false,490          "can_wiki": false,491          "read": true,492          "user_title": "",493          "bookmarked": false,494          "actions_summary": [],495          "moderator": false,496          "admin": false,497          "staff": false,498          "user_id": 18278,499          "hidden": false,500          "trust_level": 1,501          "deleted_at": null,502          "user_deleted": false,503          "edit_reason": null,504          "can_view_edit_history": true,505          "wiki": false,506          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/1",507          "can_accept_answer": false,508          "can_unaccept_answer": false,509          "accepted_answer": false,510          "topic_accepted_answer": null,511          "can_vote": false512        },513        {514          "id": 433078,515          "name": "",516          "username": "ptrblck",517          "avatar_template": "/user_avatar/discuss.pytorch.org/ptrblck/{size}/1823_2.png",518          "created_at": "2024-02-15T04:24:04.290Z",519          "cooked": "<p>Typical DDP setups use a <code>DistributedSampler</code> to avoid reusing the same samples and to split them among the ranks. Are you using such a sampler already?</p>",520          "post_number": 2,521          "post_type": 1,522          "posts_count": 8,523          "updated_at": "2024-02-15T04:24:04.290Z",524          "reply_count": 1,525          "reply_to_post_number": null,526          "quote_count": 0,527          "incoming_link_count": 5,528          "reads": 10,529          "readers_count": 9,530          "score": 32.0,531          "yours": false,532          "topic_id": 197125,533          "topic_slug": "what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus",534          "display_username": "",535          "primary_group_name": null,536          "flair_name": null,537          "flair_url": null,538          "flair_bg_color": null,539          "flair_color": null,540          "flair_group_id": null,541          "badges_granted": [],542          "version": 1,543          "can_edit": false,544          "can_delete": false,545          "can_recover": false,546          "can_see_hidden_post": false,547          "can_wiki": false,548          "read": true,549          "user_title": "",550          "bookmarked": false,551          "actions_summary": [],552          "moderator": true,553          "admin": true,554          "staff": true,555          "user_id": 3534,556          "hidden": false,557          "trust_level": 2,558          "deleted_at": null,559          "user_deleted": false,560          "edit_reason": null,561          "can_view_edit_history": true,562          "wiki": false,563          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/2",564          "can_accept_answer": false,565          "can_unaccept_answer": false,566          "accepted_answer": false,567          "topic_accepted_answer": null568        },569        {570          "id": 433113,571          "name": "PopHSKE",572          "username": "PopHSKE",573          "avatar_template": "/letter_avatar_proxy/v4/letter/p/a9adbd/{size}.png",574          "created_at": "2024-02-15T13:51:05.037Z",575          "cooked": "<p>I am. To give a little more detail, I am essentially following tutorials such as <a href=\"https://github.com/pytorch/examples/blob/main/distributed/ddp-tutorial-series/multigpu_torchrun.py\" class=\"inline-onebox\" rel=\"noopener nofollow ugc\">examples/distributed/ddp-tutorial-series/multigpu_torchrun.py at main · pytorch/examples · GitHub</a>. (Imagine in this script instead of generating the random data, it is reading a text file from S3.)</p>\n<p>where for each rank (GPU when using a single instance/node with multiple GPUs) the same dataset appears to be read into memory. So, in my script I have a step that reads data from S3 into a pandas dataframe. It seems I need to do this on each rank. When doing this, is the process loading the data into GPU memory?</p>",576          "post_number": 3,577          "post_type": 1,578          "posts_count": 8,579          "updated_at": "2024-02-15T13:57:34.477Z",580          "reply_count": 1,581          "reply_to_post_number": 2,582          "quote_count": 0,583          "incoming_link_count": 0,584          "reads": 7,585          "readers_count": 6,586          "score": 6.4,587          "yours": false,588          "topic_id": 197125,589          "topic_slug": "what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus",590          "display_username": "PopHSKE",591          "primary_group_name": null,592          "flair_name": null,593          "flair_url": null,594          "flair_bg_color": null,595          "flair_color": null,596          "flair_group_id": null,597          "badges_granted": [],598          "version": 2,599          "can_edit": false,600          "can_delete": false,601          "can_recover": false,602          "can_see_hidden_post": false,603          "can_wiki": false,604          "link_counts": [605            {606              "url": "https://github.com/pytorch/examples/blob/main/distributed/ddp-tutorial-series/multigpu_torchrun.py",607              "internal": false,608              "reflection": false,609              "title": "examples/distributed/ddp-tutorial-series/multigpu_torchrun.py at main · pytorch/examples · GitHub",610              "clicks": 6611            }612          ],613          "read": true,614          "user_title": "",615          "reply_to_user": {616            "id": 3534,617            "username": "ptrblck",618            "name": "",619            "avatar_template": "/user_avatar/discuss.pytorch.org/ptrblck/{size}/1823_2.png"620          },621          "bookmarked": false,622          "actions_summary": [],623          "moderator": false,624          "admin": false,625          "staff": false,626          "user_id": 18278,627          "hidden": false,628          "trust_level": 1,629          "deleted_at": null,630          "user_deleted": false,631          "edit_reason": null,632          "can_view_edit_history": true,633          "wiki": false,634          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/3",635          "can_accept_answer": false,636          "can_unaccept_answer": false,637          "accepted_answer": false,638          "topic_accepted_answer": null639        },640        {641          "id": 433131,642          "name": "",643          "username": "ptrblck",644          "avatar_template": "/user_avatar/discuss.pytorch.org/ptrblck/{size}/1823_2.png",645          "created_at": "2024-02-15T17:42:19.338Z",646          "cooked": "<p>I assume you are loading the entire dataset into the host RAM on each rank which is a bit wasteful. A common approach would be to use a lazy loading approach. In this case you would load the dataset location or sample paths in the <code>Dataset.__init__</code> method and would load the needed sample in the <code>Dataset.__getitem__</code>. The sampler would then make sure to only load the needed samples on each rank.</p>",647          "post_number": 4,648          "post_type": 1,649          "posts_count": 8,650          "updated_at": "2024-02-15T17:42:19.338Z",651          "reply_count": 1,652          "reply_to_post_number": 3,653          "quote_count": 0,654          "incoming_link_count": 1,655          "reads": 6,656          "readers_count": 5,657          "score": 11.2,658          "yours": false,659          "topic_id": 197125,660          "topic_slug": "what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus",661          "display_username": "",662          "primary_group_name": null,663          "flair_name": null,664          "flair_url": null,665          "flair_bg_color": null,666          "flair_color": null,667          "flair_group_id": null,668          "badges_granted": [],669          "version": 1,670          "can_edit": false,671          "can_delete": false,672          "can_recover": false,673          "can_see_hidden_post": false,674          "can_wiki": false,675          "read": true,676          "user_title": "",677          "reply_to_user": {678            "id": 18278,679            "username": "PopHSKE",680            "name": "PopHSKE",681            "avatar_template": "/letter_avatar_proxy/v4/letter/p/a9adbd/{size}.png"682          },683          "bookmarked": false,684          "actions_summary": [],685          "moderator": true,686          "admin": true,687          "staff": true,688          "user_id": 3534,689          "hidden": false,690          "trust_level": 2,691          "deleted_at": null,692          "user_deleted": false,693          "edit_reason": null,694          "can_view_edit_history": true,695          "wiki": false,696          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/4",697          "can_accept_answer": false,698          "can_unaccept_answer": false,699          "accepted_answer": false,700          "topic_accepted_answer": null701        },702        {703          "id": 433140,704          "name": "PopHSKE",705          "username": "PopHSKE",706          "avatar_template": "/letter_avatar_proxy/v4/letter/p/a9adbd/{size}.png",707          "created_at": "2024-02-15T20:43:15.214Z",708          "cooked": "<p>Yes I think I am. In a script using DDP, would this mean that the data is being loaded into GPU RAM?</p>\n<p>Dataset.<strong>getitem</strong> reads from disk, is that would you mean?</p>",709          "post_number": 5,710          "post_type": 1,711          "posts_count": 8,712          "updated_at": "2024-02-15T20:43:15.214Z",713          "reply_count": 1,714          "reply_to_post_number": 4,715          "quote_count": 0,716          "incoming_link_count": 2,717          "reads": 6,718          "readers_count": 5,719          "score": 16.2,720          "yours": false,721          "topic_id": 197125,722          "topic_slug": "what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus",723          "display_username": "PopHSKE",724          "primary_group_name": null,725          "flair_name": null,726          "flair_url": null,727          "flair_bg_color": null,728          "flair_color": null,729          "flair_group_id": null,730          "badges_granted": [],731          "version": 1,732          "can_edit": false,733          "can_delete": false,734          "can_recover": false,735          "can_see_hidden_post": false,736          "can_wiki": false,737          "read": true,738          "user_title": "",739          "reply_to_user": {740            "id": 3534,741            "username": "ptrblck",742            "name": "",743            "avatar_template": "/user_avatar/discuss.pytorch.org/ptrblck/{size}/1823_2.png"744          },745          "bookmarked": false,746          "actions_summary": [],747          "moderator": false,748          "admin": false,749          "staff": false,750          "user_id": 18278,751          "hidden": false,752          "trust_level": 1,753          "deleted_at": null,754          "user_deleted": false,755          "edit_reason": null,756          "can_view_edit_history": true,757          "wiki": false,758          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/5",759          "can_accept_answer": false,760          "can_unaccept_answer": false,761          "accepted_answer": false,762          "topic_accepted_answer": null763        },764        {765          "id": 433142,766          "name": "",767          "username": "ptrblck",768          "avatar_template": "/user_avatar/discuss.pytorch.org/ptrblck/{size}/1823_2.png",769          "created_at": "2024-02-15T21:02:28.671Z",770          "cooked": "<aside class=\"quote no-group\" data-username=\"PopHSKE\" data-post=\"5\" data-topic=\"197125\">\n<div class=\"title\">\n<div class=\"quote-controls\"></div>\n<img loading=\"lazy\" alt=\"\" width=\"24\" height=\"24\" src=\"https://discuss.pytorch.org/letter_avatar_proxy/v4/letter/p/a9adbd/48.png\" class=\"avatar\"> PopHSKE:</div>\n<blockquote>\n<p>would this mean that the data is being loaded into GPU RAM?</p>\n</blockquote>\n</aside>\n<p>Not necessarily as it depends on the <code>Dataset.__getitem__</code> implementation and if you would move the data to the device (which is not the standard use case as the data is loaded on the host in the <code>Dataset</code> and moved inside the training loop to the GPU).</p>",771          "post_number": 6,772          "post_type": 1,773          "posts_count": 8,774          "updated_at": "2024-02-15T21:02:28.671Z",775          "reply_count": 1,776          "reply_to_post_number": 5,777          "quote_count": 1,778          "incoming_link_count": 0,779          "reads": 6,780          "readers_count": 5,781          "score": 21.2,782          "yours": false,783          "topic_id": 197125,784          "topic_slug": "what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus",785          "display_username": "",786          "primary_group_name": null,787          "flair_name": null,788          "flair_url": null,789          "flair_bg_color": null,790          "flair_color": null,791          "flair_group_id": null,792          "badges_granted": [],793          "version": 1,794          "can_edit": false,795          "can_delete": false,796          "can_recover": false,797          "can_see_hidden_post": false,798          "can_wiki": false,799          "read": true,800          "user_title": "",801          "bookmarked": false,802          "actions_summary": [803            {804              "id": 2,805              "count": 1806            }807          ],808          "moderator": true,809          "admin": true,810          "staff": true,811          "user_id": 3534,812          "hidden": false,813          "trust_level": 2,814          "deleted_at": null,815          "user_deleted": false,816          "edit_reason": null,817          "can_view_edit_history": true,818          "wiki": false,819          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/6",820          "can_accept_answer": false,821          "can_unaccept_answer": false,822          "accepted_answer": false,823          "topic_accepted_answer": null824        },825        {826          "id": 433148,827          "name": "PopHSKE",828          "username": "PopHSKE",829          "avatar_template": "/letter_avatar_proxy/v4/letter/p/a9adbd/{size}.png",830          "created_at": "2024-02-15T21:32:20.803Z",831          "cooked": "<p>So when a dataset (e.g. csv read into pandas) occurs in a script using DDP as in the tutorial above ( <a href=\"https://github.com/pytorch/examples/blob/main/distributed/ddp-tutorial-series/multigpu_torchrun.py\" class=\"inline-onebox\" rel=\"noopener nofollow ugc\">examples/distributed/ddp-tutorial-series/multigpu_torchrun.py at main · pytorch/examples · GitHub</a>) on a single instance with multiple GPUs like this:</p>\n<p>df = pd.read_csv(‘s3://location_of_file’)<br>\nand then its loaded like into pytorch like:</p>\n<p>X = torch.tensor(df.values, dtype=torch.float32)<br>\nloader = DataLoader(X)</p>\n<p>this occurs in some non GPU memory that is somehow associated with each process (rank)?</p>",832          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"user_deleted": false,887          "edit_reason": null,888          "can_view_edit_history": true,889          "wiki": false,890          "post_url": "/t/what-memory-is-used-when-downloading-data-on-each-rank-multiple-gpus/197125/7",891          "can_accept_answer": false,892          "can_unaccept_answer": false,893          "accepted_answer": false,894          "topic_accepted_answer": null895        },896        {897          "id": 433153,898          "name": "",899          "username": "ptrblck",900          "avatar_template": "/user_avatar/discuss.pytorch.org/ptrblck/{size}/1823_2.png",901          "created_at": "2024-02-15T22:15:04.022Z",902          "cooked": "<aside class=\"quote no-group\" data-username=\"PopHSKE\" data-post=\"7\" data-topic=\"197125\">\n<div class=\"title\">\n<div class=\"quote-controls\"></div>\n<img loading=\"lazy\" alt=\"\" width=\"24\" height=\"24\" src=\"https://discuss.pytorch.org/letter_avatar_proxy/v4/letter/p/a9adbd/48.png\" class=\"avatar\"> PopHSKE:</div>\n<blockquote>\n<p>this occurs in some non GPU memory</p>\n</blockquote>\n</aside>\n<p>Yes, in host RAM.</p>\n<aside class=\"quote no-group\" data-username=\"PopHSKE\" data-post=\"7\" data-topic=\"197125\">\n<div class=\"title\">\n<div class=\"quote-controls\"></div>\n<img loading=\"lazy\" alt=\"\" width=\"24\" height=\"24\" src=\"https://discuss.pytorch.org/letter_avatar_proxy/v4/letter/p/a9adbd/48.png\" class=\"avatar\"> PopHSKE:</div>\n<blockquote>\n<p>that is somehow associated with each process (rank)?</p>\n</blockquote>\n</aside>\n<p>It’s just the RAM available in your system that can be used by all processes.</p>",903          "post_number": 8,904          "post_type": 1,905          "posts_count": 8,906          "updated_at": "2024-02-15T22:15:04.022Z",907          "reply_count": 0,908          "reply_to_post_number": 7,909          "quote_count": 1,910          "incoming_link_count": 0,911          "reads": 5,912          "readers_count": 4,913          "score": 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