Tag: Impl

python – having problem with multi-gpu in pytorch transformer

I am currently trying to make a translation model with Trnasformer model through PyTorch. Since I have 2 GPUs (2080ti x 2) available for training, I want to train the model through multi-gpu. Currently, the gpu is assigned to 0 and 1 respectively. The way I use multi-gpu is to…

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GPU inference doesn’t work when importing open3d

Thanks for your error report and we appreciate it a lot. Checklist I have searched related issues but cannot get the expected help. I have read the FAQ documentation but cannot get the expected help. The bug has not been fixed in the latest version. Describe the bug The GPU…

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Struts Problem Report

Struts Problem Report Struts Problem Report Struts has detected an unhandled exception: Messages: actions.Fusions.fusion?geneNameA=ZBTB1&geneNameB=MTHFD1() File: java/lang/Class.java Line number: 1,786 Stacktraces java.lang.NoSuchMethodException: actions.Fusions.fusion?geneNameA=ZBTB1&geneNameB=MTHFD1() java.lang.Class.getMethod(Class.java:1786) org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.getActionMethod(AnnotationValidationInterceptor.java:75) org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept(AnnotationValidationInterceptor.java:47) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:138) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:238) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:238) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:191) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) org.apache.struts2.interceptor.MultiselectInterceptor.intercept(MultiselectInterceptor.java:75) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:90) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploadInterceptor.java:252) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(ModelDrivenInterceptor.java:100) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ScopedModelDrivenInterceptor.intercept(ScopedModelDrivenInterceptor.java:141) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ChainingInterceptor.intercept(ChainingInterceptor.java:145) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:171)…

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Convert ONNX RuntimeError: tin_shift_forward_impl: implementation for device cpu not found.

when convert tin to onnx meet this issue: RuntimeError: tin_shift_forward_impl: implementation for device cpu not found. env:sys.platform: linuxPython: 3.8.10 (default, Jun 2 2021, 10:49:15) [GCC 9.4.0]CUDA available: TrueGPU 0,1: Tesla T4CUDA_HOME: /usr/local/cudaNVCC: Cuda compilation tools, release 11.4, V11.4.120GCC: x86_64-linux-gnu-gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0PyTorch: 1.9.1+cu111PyTorch compiling details: PyTorch built with: GCC 7.3…

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python 3.x – PySpark on Jupyterhub K8s || Unable to query data || Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Pyspark Version: 2.4.5 Hive Version: 1.2 Hadoop Version: 2.7 AWS-SDK Jar: 1.7.4 Hadoop-AWS: 2.7.3 When I am trying to show data I am getting Class org.apache.hadoop.fs.s3a.S3AFileSystem not found while I am passing all the information which all are required. I passed all three for this config fs.s3.aws.credentials.provider org.apache.hadoop.fs.s3a.BasicAWSCredentialsProvider com.amazonaws.auth.InstanceProfileCredentialsProvider com.amazonaws.auth.EnvironmentVariableCredentialsProvider…

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python – Ray training with PyTorch and PyTorchLightning raise ValueError(“Expected a parent”)

Want to improve this question? Update the question so it’s on-topic for Cross Validated. Closed 11 hours ago. I have a code that has a data module and a model and I am training my model with Ray trainer, here is my code: class…

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Running rstudio (but not R alone) inside of a conda environment complains about finding Rccp.so

I find that when I try to load some packages in a conda environement, when using rstudio (but not when I’m using R directly), I get an error message about a missing Rcpp.so file. I activate my conda environment (which is running R version 4.1), open RStudio (which I installed…

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Pymc3 linker error – v3

Hi all,I have been using pymc3 for about a year. A few months ago I changed from an intel mac to an M1 mac. Suddenly, I can’t use pymc3 anymore. I keep getting the following error that I have no idea how to interpret: You can find the C code…

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Gromacs: src/gromacs/selection/selmethod.cpp File Reference

#include “gmxpre.h” #include “selmethod.h” #include <cctype> #include <cstdarg> #include “gromacs/utility/arraysize.h” #include “gromacs/utility/cstringutil.h” #include “gromacs/utility/exceptions.h” #include “gromacs/utility/stringutil.h” #include “selmethod-impl.h” #include “symrec.h” This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements functions in selmethod.h. Author Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com static void  report_error (FILE *fp, const char…

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File “sage/symbolic/pynac_impl.pxi”, Exception. Unhandled SIGSEGV: A segmentation fault occurred

I am not sure if this is a bug in Python or sagemath. Using sagemath 9.5 on Linux Arch. I’ll describe the problem in words, then given MWE to reproduce it. I have an integrand integrand = “F(x)*(-x^2+x)^(1/2)” as string. I pass it to a subprocess using multiprocessing. When I…

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No plan found in TAP output

On Thu, 23 Dec 2021 21:59:45 +0100, Paul Gevers wrote: > With a recent upload of libio-async-perl the autopkgtest of libio-async-perl > fails in testing on ppc64el when that autopkgtest is run with the binary > packages of libio-async-perl from unstable. It passes when run with only > packages from…

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[PATCH net-next v2 3/3] net: amd-xgbe: Disable the CDR workaround path for Yellow Carp Devices

[PATCH net-next v2 3/3] net: amd-xgbe: Disable the CDR workaround path for Yellow Carp Devices – Raju Rangoju From: Raju Rangoju <rrangoju@amd.com> To: <thomas.lendacky@amd.com>, <davem@davemloft.net>, <kuba@kernel.org> Cc: <netdev@vger.kernel.org>, <Shyam-sundar.S-k@amd.com>, <Sudheesh.Mavila@amd.com>, <Raju.Rangoju@amd.com> Subject: [PATCH net-next v2 3/3] net: amd-xgbe: Disable the CDR workaround path for Yellow Carp Devices Date: Mon, 20…

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Gromacs: src/gromacs/gmxpreprocess Directory Reference

Directory dependency graph for gmxpreprocess: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Directories directory   tests   Files file   add_par.c   file   add_par.h   file   calch.c   file   calch.h   file   convparm.c   file   convparm.h  …

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Gromacs: gmx::GpuBonded::Impl Class Reference

#include <gromacs/listed-forces/gpubonded-impl.h>   Impl (const gmx_ffparams_t &ffparams, void *streamPtr)   Constructor.     ~Impl ()   Destructor, non-default needed for freeing device-side buffers.   void  updateInteractionListsAndDeviceBuffers (ArrayRef< const int > nbnxnAtomOrder, const t_idef &idef, void *xqDevice, void *forceDevice, void *fshiftDevice)   Update lists of interactions from idef suitable for the…

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RuntimeError: t == DeviceType::CUDAINTERNAL ASSERT FAILED when trying to calculate gradients

🐛 Describe the bug I am working on a constrained optimization problem using the augmented lagrange method. However, after calculating the first loss term in the optimization, I received the following error after trying to calculate the gradients with loss.backward(). /home/ihowell/Projects/validity/validity/generators/bern_vae.py:23: UserWarning: To copy construct from a tensor, it is…

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alphafold2: HHblits failed – githubmemory

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

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[jupyterhub/jupyterhub] Empty Admin page when base_url is set

Bug description If JupyterHub.base_url is set in jupyterhub_config.py, visitig the Admin tab on jupyterhub v.2.0.0 shows the empty page. Expected behaviour Without setting JupyterHub.base_url the Admin page displays the list of users: Actual behaviour The page shows only the version number: I see some errors in the log: I 2021-12-10…

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Jetson nano (B01) configures pytorch and torchvision environment + tensorrtx model transformation + deepstream deployment yolov5 (pro test available)

jetson nano To configure pytorch and torchvision Environmental Science +tensorrt Model transformation +Deepstream Deploy yolov5( Close test available ) Because a game came into contact with jetson nano, Need to use pycharm Train your own model plus yolov5 Target detection , And deployed to jetson nano On , It didn’t…

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Does PyTorch plan to support “Cpp-like” round? – #5 by Eta_C

round in PyTorch is a “Python-like” round (std::nearbyint) but not a “Cpp-like” round (std::round). It means, round([-0.5, 0.5]) would return [0, 0] but not [-1, 1]. I need “Cpp-like” round, especially when deploying my model. I check the source code and find github.com pytorch/pytorch/blob/178010455d5cd477af5a98b0e03084ffeecaecf2/aten/src/ATen/cpu/vec/vec_base.h#L469-L471 Vectorized<T> round() const { // We…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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Gromacs: Class Members – Variables

Gromacs: Class Members – Variables   – n – N : t_UmbrellaWindow , t_bb n : t_coordselection , t_methoddata_kwreal , t_methoddata_permute , t_partition , gmx_fft_fftpack , t_spheresurfacebin , t_methoddata_kwint n_alloc : t_spheresurfacebin n_at_lam : df_history_t n_dev : gmx_gpu_info_t n_dev_compatible : gmx_gpu_info_t nalloc : cu_atomdata , cl_atomdata , gmx_ana_selvalue_t , swap_compartment…

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Gromacs: gmx::KeyValueTreeTransformRulesScoped Class Reference

Public Member Functions   KeyValueTreeTransformRulesScoped (internal::KeyValueTreeTransformerImpl *impl, const KeyValueTreePath &prefix)   Internal constructor for creating the scope.     KeyValueTreeTransformRulesScoped (KeyValueTreeTransformRulesScoped &&other)   Supports returning the object from IKeyValueTreeTransformRules::scopedTransform().   KeyValueTreeTransformRulesScoped &  operator= (KeyValueTreeTransformRulesScoped &&other)   Supports returning the object from IKeyValueTreeTransformRules::scopedTransform().   IKeyValueTreeTransformRules *  rules ()   Returns the…

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bcl2fastq ERROR

bcl2fastq ERROR 1 Hi all, I have a problem. I’m running bcl2fastq software on Ubuntu, but I can’t demultiplex anything as the software gives me this error: *ERROR: bcl2fastq::common::Exception: 2021-Sep-02 12:12:34: Success (0): /home/Software/bcl2fastq/src/cxx/lib/layout/Layout.cpp(693): Throw in function void bcl2fastq::layout::handleDefaultSample(bool, bool, size_t, bcl2fastq::layout::LaneInfo&, bool&) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError> std::exception::what: Missing a…

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Pybedtools error sans

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

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