Deprecated: Return type of Requests_Cookie_Jar::offsetExists($key) should either be compatible with ArrayAccess::offsetExists(mixed $offset): bool, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Cookie/Jar.php on line 63

Deprecated: Return type of Requests_Cookie_Jar::offsetGet($key) should either be compatible with ArrayAccess::offsetGet(mixed $offset): mixed, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Cookie/Jar.php on line 73

Deprecated: Return type of Requests_Cookie_Jar::offsetSet($key, $value) should either be compatible with ArrayAccess::offsetSet(mixed $offset, mixed $value): void, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Cookie/Jar.php on line 89

Deprecated: Return type of Requests_Cookie_Jar::offsetUnset($key) should either be compatible with ArrayAccess::offsetUnset(mixed $offset): void, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Cookie/Jar.php on line 102

Deprecated: Return type of Requests_Cookie_Jar::getIterator() should either be compatible with IteratorAggregate::getIterator(): Traversable, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Cookie/Jar.php on line 111

Deprecated: Return type of Requests_Utility_CaseInsensitiveDictionary::offsetExists($key) should either be compatible with ArrayAccess::offsetExists(mixed $offset): bool, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Utility/CaseInsensitiveDictionary.php on line 40

Deprecated: Return type of Requests_Utility_CaseInsensitiveDictionary::offsetGet($key) should either be compatible with ArrayAccess::offsetGet(mixed $offset): mixed, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Utility/CaseInsensitiveDictionary.php on line 51

Deprecated: Return type of Requests_Utility_CaseInsensitiveDictionary::offsetSet($key, $value) should either be compatible with ArrayAccess::offsetSet(mixed $offset, mixed $value): void, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Utility/CaseInsensitiveDictionary.php on line 68

Deprecated: Return type of Requests_Utility_CaseInsensitiveDictionary::offsetUnset($key) should either be compatible with ArrayAccess::offsetUnset(mixed $offset): void, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Utility/CaseInsensitiveDictionary.php on line 82

Deprecated: Return type of Requests_Utility_CaseInsensitiveDictionary::getIterator() should either be compatible with IteratorAggregate::getIterator(): Traversable, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in /home/lj3i62g6dk4q/public_html/wp-includes/Requests/Utility/CaseInsensitiveDictionary.php on line 91
PyGBe: Python on the surface, GPUs at the heart. BEM solver for Electrostatics of Biomolecules :: Lorena A. Barba Group

Lorena A. Barba group

PyGBe: Python on the surface, GPUs at the heart. BEM solver for Electrostatics of Biomolecules


Warning: Undefined variable $post in /home/lj3i62g6dk4q/public_html/wp-content/themes/spruce-theme/api/figshare.php on line 57

Warning: Attempt to read property "ID" on null in /home/lj3i62g6dk4q/public_html/wp-content/themes/spruce-theme/api/figshare.php on line 57

Description

Poster presented at the GPU Technology Conference, March 2013, San Jose, CA.

It presents the PyGBe code (pronounced 'pig-bee'), which solves the linearized Poisson-Boltzmann equation using a boundary element method, BEM. The underlying dense systems are solved using a Krylov-subspace method, accelerated with a treecode to achieve O(N log N) complexity. 

The code presents a Python environment for the user, while computing all kernels in CUDA (interfaced with PyCuda), for maximum ease of use, combined with high performance on GPUs.

Acknowledgement

This research is made possible by a grant from the Office of Naval Research, Applied Computational Analysis Program (N00014-11-1-0356). LAB also acknowledges support from NSF CAREER award OCI-1149784.

Files

Links