forked from lijiext/lammps
final touches to support compiling with libcurl transparently
This commit is contained in:
Axel Kohlmeyer
parent
7a8bb5baaf
commit
741a7fe630
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@ -0,0 +1,11 @@
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# example for performing a query to the OpenKIM test database to retrieve
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# a parameter to be used in the input. here it requests the aluminium
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# lattice constant for a specific test used for a specific model and then
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# assigns it to the variable 'latconst'
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units metal
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info variables out log
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kim_query latconst get_test_result test=TE_156715955670_004 species=["Al"] model=MO_800509458712_001 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
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info variables out log
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lattice fcc ${latconst}
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@ -0,0 +1,34 @@
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LAMMPS (16 Aug 2018)
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# example for performing a query to the OpenKIM test database to retrieve
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# a parameter to be used in the input. here it requests the aluminium
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# lattice constant for a specific test used for a specific model and then
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# assigns it to the variable 'latconst'
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units metal
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info variables out log
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Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
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Printed on Mon Aug 20 18:44:24 2018
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Variable information:
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Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
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kim_query latconst get_test_result test=TE_156715955670_004 species=["Al"] model=MO_800509458712_001 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
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info variables out log
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Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
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Printed on Mon Aug 20 18:44:24 2018
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Variable information:
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Variable[ 0]: latconst , style = string , def = 4.0320827961
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Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
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lattice fcc ${latconst}
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lattice fcc 4.0320827961
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Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
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Total wall time: 0:00:00
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@ -17,13 +17,18 @@
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ifeq ($(strip $(shell pkg-config --version)),)
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$(error 'pkg-config' not found, but is required to configure the KIM API)
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endif
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kim_PREFIX := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null)
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kim_PREFIX := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,)
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kim_PREFIX := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX))
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# there is no usable libcurl installation
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ifeq ($(shell curl-config --version 2> /dev/null),)
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kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null)
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kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null)
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else
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kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null) $(shell curl-config --cflags) -DLMP_KIM_CURL
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kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null) $(shell curl-config --libs)
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endif
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ifeq ($(strip $(kim_SYSINC)),)
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$(error 'pkg-config' could not find an installed KIM API library.)
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@ -13,6 +13,12 @@ do the same thing by typing "python Install.py" from within this
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directory, or you can do it manually by following the instructions
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below.
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As of KIM API version 2, the KIM package also provides a LAMMPS command
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to perform queries through the OpenKIM web API. This feature requires
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that the CURL library (libcurl) development package and its configuration
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query tool, curl-config, are installed. The provided Makefile.lammps
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is set up to automatically detect this.
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-----------------
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Instructions:
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@ -57,36 +57,55 @@
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#include <mpi.h>
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#include <cstring>
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#include <string>
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#include "kim_query.h"
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#include "comm.h"
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#include "error.h"
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#include "input.h"
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#include "variable.h"
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#include <sys/types.h>
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#include <curl/curl.h>
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using namespace LAMMPS_NS;
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static char *do_query(char *, char *, int, MPI_Comm);
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#if defined(LMP_KIM_CURL)
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struct WriteBuf {
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char *dataptr;
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size_t sizeleft;
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};
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static char *do_query(char *, int, char **, int, MPI_Comm);
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static size_t write_callback(void *, size_t, size_t, void *);
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#endif
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/* ---------------------------------------------------------------------- */
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void KimQuery::command(int narg, char **arg)
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{
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char *model, *property, *varname, *value;
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char *varname, *function, *value;
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if (narg != 3) error->all(FLERR,"Illegal kim_query command");
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if (narg < 2) error->all(FLERR,"Illegal kim_query command");
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model = arg[0];
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property = arg[1];
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varname = arg[2];
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varname = arg[0];
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function = arg[1];
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value = do_query(model, property, comm->me, world);
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#if defined(LMP_KIM_CURL)
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value = do_query(function, narg-2, arg+2, comm->me, world);
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// check for valid result
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// on error the content of "value" is a '\0' byte
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// as the first element, and then the error message
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// that was returned by the web server
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int len = strlen(value) + 1;
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if (len == 1) {
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// TODO: store more detailed error message after \0 byte.
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error->all(FLERR,"Query of OpenKIM database failed");
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if (0 == strlen(value)) {
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char errmsg[512];
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sprintf(errmsg,"OpenKIM query failed: %s",value+1);
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error->all(FLERR,errmsg);
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}
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char **varcmd = new char*[3];
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@ -98,26 +117,119 @@ void KimQuery::command(int narg, char **arg)
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delete[] varcmd;
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delete[] value;
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#else
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error->all(FLERR,"Cannot use 'kim_query' command when KIM package "
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"is compiled without support for libcurl");
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#endif
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}
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#if defined(LMP_KIM_CURL)
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char *do_query(char *model, char *property, int rank, MPI_Comm comm)
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// copy data to the user provided data structure, optionally in increments
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size_t write_callback(void *data, size_t size, size_t nmemb, void *userp)
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{
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struct WriteBuf *buf = (struct WriteBuf *)userp;
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size_t buffer_size = size*nmemb;
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// copy chunks into the buffer for as long as there is space left
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if (buf->sizeleft) {
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size_t copy_this_much = buf->sizeleft;
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if (copy_this_much > buffer_size)
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copy_this_much = buffer_size;
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memcpy(buf->dataptr, data, copy_this_much);
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buf->dataptr += copy_this_much;
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buf->sizeleft -= copy_this_much;
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return copy_this_much;
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}
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return 0; // done
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}
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char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
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{
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char value[512], *retval;
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// only run query from rank 0
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if (rank == 0) {
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// run the web query from rank 0 only
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// fake query
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strcpy(value,(const char*)"4.25");
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if (rank == 0) {
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CURL *handle;
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CURLcode res;
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// set up and clear receive buffer
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struct WriteBuf buf;
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buf.dataptr = value;
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buf.sizeleft = 511;
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memset(value,0,512);
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// create curl web query instance
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curl_global_init(CURL_GLOBAL_DEFAULT);
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handle = curl_easy_init();
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if (handle) {
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std::string url("https://query.openkim.org/api/");
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url += qfunction;
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std::string query(arg[0]);
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for (int i=1; i < narg; ++i) {
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query += '&';
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query += arg[i];
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}
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#if LMP_DEBUG_CURL
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curl_easy_setopt(handle, CURLOPT_VERBOSE, 1L);
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#endif
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#if defined(LMP_NO_SSL_CHECK)
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// disable verifying SSL certificate and host name
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curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L);
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curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L);
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#endif
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curl_easy_setopt(handle, CURLOPT_URL, url.c_str());
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curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L);
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curl_easy_setopt(handle, CURLOPT_POSTFIELDS, query.c_str());
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curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION,write_callback);
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curl_easy_setopt(handle, CURLOPT_WRITEDATA,&buf);
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// perform OpenKIM query and check for errors
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res = curl_easy_perform(handle);
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if (res != CURLE_OK) {
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// on error we return an "empty" string but add error message after it
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value[0]= '\0';
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strcpy(value+1,curl_easy_strerror(res));
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}
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curl_easy_cleanup(handle);
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}
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curl_global_cleanup();
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}
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MPI_Bcast(value, 512, MPI_CHAR, 0, comm);
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// must make a proper copy of the query, as the stack allocation
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// will go out of scope
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// we must make a proper copy of the query, as the stack allocation
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// for "value" will go out of scope. a valid query has a '[' as
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// the first character. skip over it (and the last character ']', too)
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// an error messages starts with a '\0' character. copy that and
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// the remaining string, as that is the error message.
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int len = strlen(value) + 1;
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retval = new char[len];
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strcpy(retval,value);
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if (value[0] == '[') {
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int len = strlen(value)-1;
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retval = new char[len];
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value[len] = '\0';
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strcpy(retval,value+1);
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} else if (value[0] == '\0') {
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int len = strlen(value+1)+2;
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retval = new char[len];
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retval[0] = '\0';
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strcpy(retval+1,value+1);
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} else {
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// unknown response type. we should not get here.
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// copy response without modifications.
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int len = strlen(value)+1;
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retval = new char[len];
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strcpy(retval,value);
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}
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return retval;
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}
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#endif
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