# Cmdstanpy: Not working with google colab GPU

**URL:** <https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834>\
**Category:** CmdStan\
**Created:** [October 13, 2021, 6:39pm UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834 "2021-10-13T18:39:29Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![kyo219](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kyo219/32/12168_2.png) [@kyo219](https://discourse.mc-stan.org/u/kyo219)\
**Post date:** [October 13, 2021, 6:39pm UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/1 "2021-10-13T18:39:29Z")

</div>

I want to run cmdstan using the GPU of google colab.

While it works on the CPU, it cannot be confirmed to work on the GPU…

```

cpp_options = {
                #'STAN_THREADS' : True , 
                #'STAN_CPP_OPTIMS' : True, 
                'STAN_OPENCL' : True ,
                'OPENCL_PLATFORM_ID' : 0 ,
                'OPENCL_DEVICE_ID' : 0}

sm = cmdstanpy.CmdStanModel(stan_file="/content/gdrive/MyDrive/colab/stan_code.stan", cpp_options= cpp_options)

```

```
fit = sm.sample(data=df, chains=2, iter_warmup=500,iter_sampling=500, show_progress=True)

```

---- output ----

Chain 1 - done: 0%| | 1/1000 [07:35\<126:19:31, 455.23s/it]  
Chain 2 - warmup: 0%| | 0/1 [07:36\<?, ?it/s]

* * *

↑It’s freezing.

---

<div class="post-metadata">

**Author:** ![WardBrian](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/wardbrian/32/12078_2.png) [@WardBrian](https://discourse.mc-stan.org/u/WardBrian)\
**Post date:** [October 13, 2021, 7:11pm UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/2 "2021-10-13T19:11:12Z")

</div>

Hi @kyo219 - we have had reports in the past of the show\_progress function acting strangely in notebooks. It’s all been re-written in 1.0 which should be out soon (or if you want to do a pip install from github).

That said, if it’s working on the CPU I suspect it is another issue.

@mitzimorris - I know you’ve used cmdstanpy in Google collab. Is the issue that cmdstan itself would need to be rebuilt with these flags, or could it be an issue with external dependencies? Not sure what opencl requires

---

<div class="post-metadata">

**Author:** ![rok\_cesnovar](https://avatars.discourse-cdn.com/v4/letter/r/7bcc69/32.png) [@rok\_cesnovar](https://discourse.mc-stan.org/u/rok_cesnovar)\
**Post date:** [October 13, 2021, 7:22pm UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/3 "2021-10-13T19:22:15Z")

</div>

I dont have any familiartiy with Google Colab so not sure I can help a ton but can try. The OpenCL dependencies that are required are listed here: [14 Parallelization | CmdStan User’s Guide](https://mc-stan.org/docs/2_28/cmdstan-guide/parallelization.html#opencl)

---

<div class="post-metadata">

**Author:** ![kyo219](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kyo219/32/12168_2.png) [@kyo219](https://discourse.mc-stan.org/u/kyo219)\
**Post date:** [October 14, 2021, 10:47am UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/4 "2021-10-14T10:47:57Z")

</div>

thank you guys.

when I try

```
sudo apt install nvidia-cuda-toolkit

```

then, I got this error message.

```
Preparing to unpack .../48-nvidia-cuda-dev_9.1.85-3ubuntu1_amd64.deb ...
dpkg: error processing archive /tmp/apt-dpkg-install-1gv7Ba/48-nvidia-cuda-dev_9.1.85-3ubuntu1_amd64.deb (--unpack): trying to overwrite '/usr/include/cublas.h', which is
also in package libcublas-dev 10.2.1.243-1dpkg-deb: error: paste subprocess was killed by signal(Broken pipe)

```

---

<div class="post-metadata">

**Author:** ![kyo219](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kyo219/32/12168_2.png) [@kyo219](https://discourse.mc-stan.org/u/kyo219)\
**Post date:** [October 14, 2021, 11:05am UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/5 "2021-10-14T11:05:14Z")

</div>

my environment

```
/content# clinfo -l
Platform #0: NVIDIA CUDA
 `-- Device #0: Tesla P100-PCIE-16GB

```

```
!nvidia-smi

Thu Oct 14 10:39:31 2021       
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 470.74 Driver Version: 460.32.03 CUDA Version: 11.2 |
|-------------------------------+----------------------+----------------------+
| 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 Tesla P100-PCIE... Off | 00000000:00:04.0 Off | 0 |
| N/A 32C P0 27W / 250W | 0MiB / 16280MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+

```

```

!nvcc --version

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2020 NVIDIA Corporation
Built on Mon_Oct_12_20:09:46_PDT_2020
Cuda compilation tools, release 11.1, V11.1.105
Build cuda_11.1.TC455_06.29190527_0

```

---

<div class="post-metadata">

**Author:** ![kyo219](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kyo219/32/12168_2.png) [@kyo219](https://discourse.mc-stan.org/u/kyo219)\
**Post date:** [October 14, 2021, 3:12pm UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/6 "2021-10-14T15:12:35Z")

</div>

I also try cmdstanr in Google colab.

I got the same problem with cmdstanpy.

```
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
library(cmdstanr)
install_cmdstan(cores=4, overwrite = TRUE)

```

```
sm <- cmdstan_model("/stan_code.stan",
                        cpp_options = list(stan_opencl = TRUE))

```

its done

But . There is a problem with the sampling.

```
fit <- sm$sample(data = data, chains = 4, parallel_chains = 4,
                        opencl_ids = c(0, 0), refresh = 0)

```

```
Running MCMC with 4 parallel chains...

Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:

Chain 1 Exception: stan_code_model_namespace::log_prob: o_Tau is not symmetric. o_Tau[1,2] = inf, but o_Tau[2,1] = inf (in '/tmp/RtmpEBdlH8/model-4d182d8a1c.stan', line 43, column 8 to column 40)

Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,

Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.

.....

```

↑ freeze

---

<div class="post-metadata">

**Author:** ![kyo219](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kyo219/32/12168_2.png) [@kyo219](https://discourse.mc-stan.org/u/kyo219)\
**Post date:** [October 17, 2021, 9:05am UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/7 "2021-10-17T09:05:04Z")

</div>

when I stop sampling( freeze)

see this error message

```
Chain 3 - done: 0%| | 0/1 [01:58<?, ?it/s]Chain 3 processing error, non-zero return code 1
 error message:
	Can't open specified file, "/tmp/tmpht4im148/jwfqze60.json"

Chain 4 - done: 0%| | 0/1 [01:58<?, ?it/s]Chain 4 processing error, non-zero return code 1
 error message:
	Can't open specified file, "/tmp/tmpht4im148/jwfqze60.json"

```

---

<div class="post-metadata">

**Author:** ![kyo219](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kyo219/32/12168_2.png) [@kyo219](https://discourse.mc-stan.org/u/kyo219)\
**Post date:** [October 19, 2021, 5:16am UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/8 "2021-10-19T05:16:40Z")

</div>

compile error

```
INFO:cmdstanpy:compiling stan program, exe file: /content/drive/MyDrive/eiv_gpu/m4_non
INFO:cmdstanpy:compiler options: stanc_options=None, cpp_options={'STAN_THREADS': True, 'STAN_OPENCL': 'TRUE', 'OPENCL_PLATFORM_ID': 0, 'OPENCL_DEVICE_ID': 0}
ERROR:cmdstanpy:file /content/drive/MyDrive/eiv_gpu/m4_non.stan, exception ERROR
 In file included from stan/lib/stan_math/stan/math/opencl/prim.hpp:200:0,
                 from stan/lib/stan_math/stan/math/prim.hpp:7,
                 from stan/src/stan/io/dump.hpp:7,
                 from src/cmdstan/command.hpp:30,
                 from src/cmdstan/main.cpp:1:
stan/lib/stan_math/stan/math/opencl/prim/normal_lcdf.hpp: In function ‘stan::return_type_t<T_y_cl, T_loc_cl, T_scale_cl> stan::math::normal_lcdf(const T_y_cl&, const T_loc_cl&, const T_scale_cl&)’:
stan/lib/stan_math/stan/math/opencl/prim/normal_lcdf.hpp:215:39: error: the value of ‘stan::math::internal::opencl_normal_lcdf_impl’ is not usable in a constant expression
   auto lcdf_n = opencl_code<internal::opencl_normal_lcdf_impl>(
                                       ^ ~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/opencl/prim/normal_lcdf.hpp:16:12: note: ‘stan::math::internal::opencl_normal_lcdf_impl’ was not declared ‘constexpr’
 const char opencl_normal_lcdf_impl[] = STRINGIFY(
            ^ ~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/opencl/prim/normal_lcdf.hpp:221:31: error: the value of ‘stan::math::internal::opencl_normal_lcdf_ldncdf_impl’ is not usable in a constant expression
       = opencl_code<internal::opencl_normal_lcdf_ldncdf_impl>(
                               ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/opencl/prim/normal_lcdf.hpp:59:12: note: ‘stan::math::internal::opencl_normal_lcdf_ldncdf_impl’ was not declared ‘constexpr’
 const char opencl_normal_lcdf_ldncdf_impl[] = STRINGIFY(
            ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stan/lib/stan_math/stan/math/opencl/prim.hpp:249:0,
                 from stan/lib/stan_math/stan/math/prim.hpp:7,
                 from stan/src/stan/io/dump.hpp:7,
                 from src/cmdstan/command.hpp:30,
                 from src/cmdstan/main.cpp:1:
stan/lib/stan_math/stan/math/opencl/prim/std_normal_lcdf.hpp: In function ‘stan::return_type_t<T> stan::math::std_normal_lcdf(const T_y_cl&)’:
stan/lib/stan_math/stan/math/opencl/prim/std_normal_lcdf.hpp:201:29: error: the value of ‘stan::math::internal::opencl_std_normal_lcdf_impl’ is not usable in a constant expression
       opencl_code<internal::opencl_std_normal_lcdf_impl>(
                             ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/opencl/prim/std_normal_lcdf.hpp:16:12: note: ‘stan::math::internal::opencl_std_normal_lcdf_impl’ was not declared ‘constexpr’
 const char opencl_std_normal_lcdf_impl[] = STRINGIFY(
            ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/opencl/prim/std_normal_lcdf.hpp:205:39: error: the value of ‘stan::math::internal::opencl_std_normal_lcdf_dnlcdf’ is not usable in a constant expression
   auto dnlcdf = opencl_code<internal::opencl_std_normal_lcdf_dnlcdf>(
                                       ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/opencl/prim/std_normal_lcdf.hpp:52:12: note: ‘stan::math::internal::opencl_std_normal_lcdf_dnlcdf’ was not declared ‘constexpr’
 const char opencl_std_normal_lcdf_dnlcdf[] = STRINGIFY(
            ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stan/lib/stan_math/stan/math/opencl/kernel_generator.hpp:136:0,
                 from stan/lib/stan_math/stan/math/opencl/rev/vari.hpp:7,
                 from stan/lib/stan_math/stan/math/rev/core/var.hpp:5,
                 from stan/lib/stan_math/stan/math/rev/core/profiling.hpp:6,
                 from src/cmdstan/write_profiling.hpp:4,
                 from src/cmdstan/command.hpp:21,
                 from src/cmdstan/main.cpp:1:
stan/lib/stan_math/stan/math/opencl/kernel_generator/multi_result_kernel.hpp: In instantiation of ‘stan::math::results_cl<T_results>::operator=(const stan::math::expressions_cl<T_expressions ...>&)::<lambda(auto:20 ...)> [with auto:20 = {std::integral_constant<long unsigned int, 0ul>}; T_expressions = {const stan::math::constant_<double>&}; <template-parameter-2-2> = void; T_results = {stan::math::matrix_cl<double>&}]’:

.....

make: *** [src/cmdstan/main_threads_opencl.o] Error 1 
ERROR:cmdstanpy:model compilation failed

```

---

<div class="post-metadata">

**Author:** ![rok\_cesnovar](https://avatars.discourse-cdn.com/v4/letter/r/7bcc69/32.png) [@rok\_cesnovar](https://discourse.mc-stan.org/u/rok_cesnovar)\
**Post date:** [October 19, 2021, 7:16am UTC](https://discourse.mc-stan.org/t/cmdstanpy-not-working-with-google-colab-gpu/24834/9 "2021-10-19T07:16:04Z")

</div>

Can you try and compile this GLM example model:

```stan
data {
  int<lower=1> k;
  int<lower=0> n;
  matrix[n, k] X;
  int y[n];
}
parameters {
  vector[k] beta;
  real alpha;
}
model {
  target += std_normal_lpdf(beta);
  target += std_normal_lpdf(alpha);
  target += bernoulli_logit_glm_lpmf(y | X, alpha, beta);
}

```