Error while using CPPPotential

SANJAY BHANDARKAR

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Jun 1, 2023, 5:55:09 AM6/1/23

to hoomd-users

Dear everone,

I am trying to run an example script which gives me an error. Could someone please let me know how to resolve this?

My Code-

# The square well potential
r_interaction = 1.1
evaluate_square_well = f'''float rsq = dot(r_ij, r_ij);
if (rsq < {r_interaction * r_interaction}f)
return param_array[0];
else
return 0.0f;
'''
square_well = hoomd.hpmc.pair.user.CPPPotential(r_cut=r_interaction,
code=evaluate_square_well,
param_array=[-1])

# hpmc.Sphere provides the hard sphere part of the potential
mc = hoomd.hpmc.integrate.Sphere()
mc.shape['S'] = dict(diameter=1.0)

The error -

RuntimeError: Error compiling JIT code:

#include <stdio.h>
#include "hoomd/HOOMDMath.h"
#include "hoomd/VectorMath.h"

// param_array (singlet class) or param_array_isotropic
// and param_array_constituent (union class) are
// allocated by the library
float *param_array;

using namespace hoomd;

extern "C"
{
float eval(const vec3<float>& r_ij,
unsigned int type_i,
const quat<float>& q_i,
float d_i,
float charge_i,
unsigned int type_j,
const quat<float>& q_j,
float d_j,
float charge_j)
{
float rsq = dot(r_ij, r_ij);
if (rsq < 1.2100000000000002f)
return param_array[0];
else
return 0.0f;

}
}

In file included from code.cc:3:
/home/anaconda3/lib/python3.10/site-packages/hoomd/include/hoomd/HOOMDMath.h:33:10: fatal error: 'cmath' file not found
#include <cmath>
^~~~~~~
Error generating code.
1 error generated.

Joshua Anderson

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Jun 1, 2023, 7:48:59 AM6/1/23

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Sanjay,

Please try this with a mambaforge, miniforge, or miniconda install (with conda-forge set as the default channel). The anaconda distribution pins many packages to versions that are not compatible with hoomd.

If you get the same behavior, then please let me know what platform you are running on and provide the output of `conda list`.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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SANJAY BHANDARKAR

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Jun 7, 2023, 4:28:46 AM6/7/23

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I get the same error even with a miniconda install. I am running on Ubuntu 22.04.2.

This is the output of conda-list -

# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
binutils_impl_linux-64 2.38 h2a08ee3_1
boltons 23.0.0 py310h06a4308_0
brotlipy 0.7.0 py310h7f8727e_1002
bzip2 1.0.8 h7b6447c_0
ca-certificates 2023.5.7 hbcca054_0 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h5eee18b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
clang 14.0.6 h06a4308_1
clang-14 14.0.6 default_hc6dbbc7_1
clangxx 14.0.6 default_hc6dbbc7_1
conda 23.5.0 py310hff52083_1 conda-forge
conda-content-trust 0.1.3 py310h06a4308_0
conda-package-handling 2.0.2 py310h06a4308_0
conda-package-streaming 0.7.0 py310h06a4308_0
cryptography 39.0.1 py310h9ce1e76_0
gcc_impl_linux-64 7.5.0 habd7529_20 conda-forge
gsd 2.9.0 pypi_0 pypi
hoomd 3.11.0 cpu_py310h9445866_0 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 3.4 py310h06a4308_0
jsonpatch 1.32 pyhd3eb1b0_0
jsonpointer 2.1 pyhd3eb1b0_0
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
ld_impl_linux-64 2.38 h1181459_1
libblas 3.9.0 17_linux64_openblas conda-forge
libcblas 3.9.0 17_linux64_openblas conda-forge
libclang-cpp 14.0.6 default_hc6dbbc7_1
libclang-cpp14 14.0.6 default_hc6dbbc7_1
libcxx 14.0.6 h83ecd13_0
libcxxabi 14.0.6 h06a4308_0
libffi 3.4.2 h6a678d5_6
libgcc-devel_linux-64 7.5.0 hda03d7c_20 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libhwloc 2.9.1 hd6dc26d_0 conda-forge
liblapack 3.9.0 17_linux64_openblas conda-forge
libllvm14 14.0.6 hdb19cb5_3
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libstdcxx-devel_linux-64 13.1.0 he3cc6c4_0 conda-forge
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libuuid 1.41.5 h5eee18b_0
libxml2 2.10.3 hcbfbd50_0
ncurses 6.4 h6a678d5_0
numpy 1.24.3 py310ha4c1d20_0 conda-forge
openssl 1.1.1u hd590300_0 conda-forge
packaging 23.0 py310h06a4308_0
pip 23.0.1 py310h06a4308_0
pluggy 1.0.0 py310h06a4308_1
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.4 py310h5eee18b_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 23.0.0 py310h06a4308_0
pysocks 1.7.1 py310h06a4308_0
python 3.10.10 h7a1cb2a_2
python_abi 3.10 2_cp310 conda-forge
readline 8.2 h5eee18b_0
requests 2.28.1 py310h06a4308_1
ruamel.yaml 0.17.21 py310h5eee18b_0
ruamel.yaml.clib 0.2.6 py310h5eee18b_1
setuptools 65.6.3 py310h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.1 h5eee18b_0
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tbb 2021.9.0 hf52228f_0 conda-forge
tk 8.6.12 h1ccaba5_0
toolz 0.12.0 py310h06a4308_0
tqdm 4.65.0 py310h2f386ee_0
tzdata 2023c h04d1e81_0
urllib3 1.26.15 py310h06a4308_0
wheel 0.38.4 py310h06a4308_0
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h5eee18b_0
zstandard 0.19.0 py310h5eee18b_0

Joshua Anderson

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Jun 7, 2023, 7:48:29 AM6/7/23

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Sanjay,

Your install includes clang (and many other packages) from the default channel:

clang 14.0.6 h06a4308_1

Specifically, the conda-forge clang is patched to search for headers like cmath in the conda-forge provided sysroot package. Read the conda-forge documentation for instructions on how to use miniconda appropriately with conda-forge.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/4a1525c5-d7ed-4ec3-b1a1-a69d2b84b806n%40googlegroups.com.

SANJAY BHANDARKAR

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Jun 7, 2023, 8:18:37 AM6/7/23

to hoomd-users

I tried it with miniforge install.

This is the output od conda list -

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge

binutils_impl_linux-64 2.40 hf600244_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py310h5764c6d_1005 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge

ca-certificates 2023.5.7 hbcca054_0 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge

cffi 1.15.1 py310h255011f_3 conda-forge
charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
clang 14.0.6 ha770c72_1 conda-forge
clang-14 14.0.6 default_h7634d5b_1 conda-forge
clangxx 14.0.6 default_h1e1816b_1 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 23.5.0 py310hff52083_1 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge
cryptography 40.0.1 py310h34c0648_0 conda-forge
gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge

gsd 2.9.0 pypi_0 pypi
hoomd 3.11.0 cpu_py310h9445866_0 conda-forge

icu 72.1 hcb278e6_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge

libblas 3.9.0 17_linux64_openblas conda-forge
libcblas 3.9.0 17_linux64_openblas conda-forge

libclang-cpp 14.0.6 default_h7634d5b_1 conda-forge
libclang-cpp14 14.0.6 default_h7634d5b_1 conda-forge
libcxx 14.0.6 hf52228f_0 conda-forge
libcxxabi 14.0.6 ha770c72_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge

libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge

libgomp 12.2.0 h65d4601_19 conda-forge
libhwloc 2.9.1 cpu_h1633a84_5 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 17_linux64_openblas conda-forge
libllvm14 14.0.6 hcd5def8_3 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libsanitizer 12.2.0 h46fd767_19 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libstdcxx-devel_linux-64 13.1.0 he3cc6c4_0 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxml2 2.11.4 h0d562d8_0 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.24.3 py310ha4c1d20_0 conda-forge
openssl 3.1.1 hd590300_1 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pip 23.0.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.4 py310h5764c6d_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.10 he550d4f_0_cpython conda-forge
python_abi 3.10 3_cp310 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.28.2 pyhd8ed1ab_1 conda-forge
ruamel.yaml 0.17.21 py310h1fa729e_3 conda-forge
ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge
setuptools 65.6.3 pyhd8ed1ab_0 conda-forge

sysroot_linux-64 2.12 he073ed8_15 conda-forge
tbb 2021.9.0 hf52228f_0 conda-forge

tk 8.6.12 h27826a3_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
urllib3 1.26.15 pyhd8ed1ab_0 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zstandard 0.19.0 py310hdeb6495_1 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge

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