diff --git a/ChangeLog.md b/ChangeLog.md new file mode 100644 --- /dev/null +++ b/ChangeLog.md @@ -0,0 +1,5 @@ +# Revision history for drmaa + +## 0.1.0.0 -- YYYY-mm-dd + +* First version. Released on an unsuspecting world. diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,30 @@ +Copyright (c) 2015, Kai Zhang + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + + * Neither the name of Kai Zhang nor the names of other + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,2 @@ +import Distribution.Simple +main = defaultMain diff --git a/drmaa.cabal b/drmaa.cabal new file mode 100644 --- /dev/null +++ b/drmaa.cabal @@ -0,0 +1,37 @@ +-- Initial drmaa.cabal generated by cabal init. For further documentation, +-- see http://haskell.org/cabal/users-guide/ + +name: drmaa +version: 0.1.0.0 +synopsis: A simple Haskell bindings to DRMAA C library. +description: A simple Haskell bindings to DRMAA C library. +license: BSD3 +license-file: LICENSE +author: Kai Zhang +maintainer: kai@kzhang.org +-- copyright: +category: Language +build-type: Simple +extra-source-files: ChangeLog.md +cabal-version: >=1.10 + +library + ghc-options: -Wall + exposed-modules: + DRMAA + + -- other-modules: + -- other-extensions: + build-depends: + base >=4.7 && <5.0 + , bytestring + , binary + , async + , inline-c + , text + , shelly + + hs-source-dirs: src + c-sources: src/DRMAA.c + extra-libraries: drmaa + default-language: Haskell2010 diff --git a/src/DRMAA.c b/src/DRMAA.c new file mode 100644 --- /dev/null +++ b/src/DRMAA.c @@ -0,0 +1,146 @@ + +#include "stddef.h" + +#include "stdio.h" + +#include "drmaa.h" + +int inline_c_DRMAA_0_54e600eaaa1f15b2d247a7799eeb2c2626774aa9(char * ptr_inline_c_0) { + + int errnum = 0; + errnum = drmaa_init (NULL, ptr_inline_c_0, DRMAA_ERROR_STRING_BUFFER); + if (errnum != DRMAA_ERRNO_SUCCESS) { + return 1; + } + return 0; + +} + + +int inline_c_DRMAA_1_df791815daa185d543e0513c42f96dbbd8b8b214() { + + char error[DRMAA_ERROR_STRING_BUFFER]; + int errnum = 0; + errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER); + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error); + return 1; + } + return 0; + +} + + +int inline_c_DRMAA_2_8569c20fd54d45f727dd1560458a1febedbc42e1(char * wd_inline_c_0, const char ** envPtr_inline_c_1, char * native_inline_c_2, char * c_exec_inline_c_3, const char ** aptr_inline_c_4) { + + int exception = 0; + char error[DRMAA_ERROR_STRING_BUFFER]; + int errnum = 0; + drmaa_job_template_t *jt = NULL; + + errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not create job template: %s\n", error); + } else { + /* set options */ + errnum = drmaa_set_attribute (jt, DRMAA_WD, wd_inline_c_0, + error, DRMAA_ERROR_STRING_BUFFER); + errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ENV, envPtr_inline_c_1, + error, DRMAA_ERROR_STRING_BUFFER); + errnum = drmaa_set_attribute (jt, DRMAA_NATIVE_SPECIFICATION, native_inline_c_2, + error, DRMAA_ERROR_STRING_BUFFER); + + errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, c_exec_inline_c_3, + error, DRMAA_ERROR_STRING_BUFFER); + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not set attribute \"%s\": %s\n", + DRMAA_REMOTE_COMMAND, error); + } else { + errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, aptr_inline_c_4, error, + DRMAA_ERROR_STRING_BUFFER); + } + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not set attribute \"%s\": %s\n", + DRMAA_REMOTE_COMMAND, error); + } else { + char jobid[DRMAA_JOBNAME_BUFFER]; + char jobid_out[DRMAA_JOBNAME_BUFFER]; + int status = 0; + drmaa_attr_values_t *rusage = NULL; + + errnum = drmaa_run_job (jobid, DRMAA_JOBNAME_BUFFER, jt, error, + DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not submit job: %s\n", error); + exception = 1; + } else { + printf ("Your job has been submitted with id %s\n", jobid); + + errnum = drmaa_wait (jobid, jobid_out, DRMAA_JOBNAME_BUFFER, &status, + DRMAA_TIMEOUT_WAIT_FOREVER, &rusage, error, + DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not wait for job: %s\n", error); + exception = 1; + } else { + char usage[DRMAA_ERROR_STRING_BUFFER]; + int aborted = 0; + + drmaa_wifaborted(&aborted, status, NULL, 0); + + if (aborted == 1) { + printf("Job %s never ran\n", jobid); + exception = 1; + } else { + int exited = 0; + + drmaa_wifexited(&exited, status, NULL, 0); + + if (exited == 1) { + int exit_status = 0; + + drmaa_wexitstatus(&exit_status, status, NULL, 0); + printf("Job %s finished regularly with exit status %d\n", jobid, exit_status); + exception = exit_status; + } else { + int signaled = 0; + + drmaa_wifsignaled(&signaled, status, NULL, 0); + + if (signaled == 1) { + char termsig[DRMAA_SIGNAL_BUFFER+1]; + + drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, status, NULL, 0); + printf("Job %s finished due to signal %s\n", jobid, termsig); + } else { + printf("Job %s finished with unclear conditions\n", jobid); + } + } /* else */ + } /* else */ + + printf ("Job Usage:\n"); + + while (drmaa_get_next_attr_value (rusage, usage, DRMAA_ERROR_STRING_BUFFER) == DRMAA_ERRNO_SUCCESS) { + printf (" %s\n", usage); + } + + drmaa_release_attr_values (rusage); + } /* else */ + } /* else */ + } /* else */ + + errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not delete job template: %s\n", error); + } + } /* else */ + + return exception; + +} + diff --git a/src/DRMAA.hs b/src/DRMAA.hs new file mode 100644 --- /dev/null +++ b/src/DRMAA.hs @@ -0,0 +1,214 @@ +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE QuasiQuotes #-} +{-# LANGUAGE TemplateHaskell #-} +module DRMAA where + +import Control.Exception (bracket_, bracket) +import qualified Data.Text as T +import Shelly hiding (FilePath, withTmpDir) + +import Foreign.C.String +import Foreign.Marshal.Alloc +import Foreign.Marshal.Array +import Foreign.Ptr +import qualified Language.C.Inline as C + +C.include "stddef.h" +C.include "stdio.h" +C.include "drmaa.h" + +withTmpFile :: FilePath -> (FilePath -> IO a) -> IO a +withTmpFile dir = bracket create delete + where + create = shelly $ fmap (T.unpack . head . T.lines) $ silently $ + run "mktemp" [T.pack $ dir ++ "/tmp_file_XXXXXXXX_delete.me"] + delete = shelly . rm_f . fromText . T.pack + +withTmpDir :: FilePath -> (FilePath -> IO a) -> IO a +withTmpDir dir = bracket create delete + where + create = shelly $ fmap (T.unpack . head . T.lines) $ silently $ + run "mktemp" ["-d", T.pack $ dir ++ "/tmp_dir_XXXXXXXX_delete.me"] + delete = shelly . rm_rf . fromText . T.pack + +withSGESession :: IO a -> IO a +withSGESession f = bracket_ drmaaInit drmaaExit f + +drmaaScript :: String -> DrmaaAttribute -> IO () +drmaaScript script config = bracket + (shelly $ fmap (T.unpack . head . T.lines) $ silently $ run "mktemp" [template]) + (shelly . rm . fromText . T.pack) + $ \tmpFl -> do + writeFile tmpFl $ "#!/bin/sh\n" ++ script + shelly $ run_ "chmod" ["+x", T.pack tmpFl] + drmaaRun tmpFl [] config + where + template = T.pack $ drmaa_wd config ++ "/drmaa_script.XXXXXXXX.delete.me.sh" + +-- | Initialize a session +drmaaInit :: IO () +drmaaInit = alloca $ \ptr -> do + status <- [C.block| int { + int errnum = 0; + errnum = drmaa_init (NULL, $(char* ptr), DRMAA_ERROR_STRING_BUFFER); + if (errnum != DRMAA_ERRNO_SUCCESS) { + return 1; + } + return 0; + }|] + case status of + 0 -> putStrLn "DRMAA session started" + _ -> peekCString ptr >>= error + +drmaaExit :: IO () +drmaaExit = do + r <- [C.block| int { + char error[DRMAA_ERROR_STRING_BUFFER]; + int errnum = 0; + errnum = drmaa_exit (error, DRMAA_ERROR_STRING_BUFFER); + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not shut down the DRMAA library: %s\n", error); + return 1; + } + return 0; + }|] + case r of + 0 -> putStrLn "DRMAA session closed" + _ -> error "Exit 1" + +data DrmaaAttribute = DrmaaAttribute + { drmaa_wd :: !FilePath + , drmaa_env :: ![(String, String)] + , drmaa_native :: !String + } deriving (Show, Read) + +defaultDrmaaConfig :: DrmaaAttribute +defaultDrmaaConfig = DrmaaAttribute + { drmaa_wd = "./" + , drmaa_env = [ ("DRMAA_ENV_HAS_SET", "True") ] + , drmaa_native = "" + } + +drmaaRun :: FilePath -> [String] -> DrmaaAttribute -> IO () +drmaaRun exec args config = do + c_exec <- newCString exec + c_args <- mapM newCString args + + -- options + wd <- newCString $ drmaa_wd config + env <- mapM (\(a,b) -> newCString $ a ++ "=" ++ b) $ drmaa_env config + native <- newCString $ drmaa_native config + + e <- withArray (c_args++[nullPtr]) $ \aptr -> + withArray (env ++ [nullPtr]) $ \envPtr -> do + [C.block| int { + int exception = 0; + char error[DRMAA_ERROR_STRING_BUFFER]; + int errnum = 0; + drmaa_job_template_t *jt = NULL; + + errnum = drmaa_allocate_job_template (&jt, error, DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not create job template: %s\n", error); + } else { + /* set options */ + errnum = drmaa_set_attribute (jt, DRMAA_WD, $(char* wd), + error, DRMAA_ERROR_STRING_BUFFER); + errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ENV, $(const char** envPtr), + error, DRMAA_ERROR_STRING_BUFFER); + errnum = drmaa_set_attribute (jt, DRMAA_NATIVE_SPECIFICATION, $(char* native), + error, DRMAA_ERROR_STRING_BUFFER); + + errnum = drmaa_set_attribute (jt, DRMAA_REMOTE_COMMAND, $(char* c_exec), + error, DRMAA_ERROR_STRING_BUFFER); + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not set attribute \"%s\": %s\n", + DRMAA_REMOTE_COMMAND, error); + } else { + errnum = drmaa_set_vector_attribute (jt, DRMAA_V_ARGV, $(const char** aptr), error, + DRMAA_ERROR_STRING_BUFFER); + } + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not set attribute \"%s\": %s\n", + DRMAA_REMOTE_COMMAND, error); + } else { + char jobid[DRMAA_JOBNAME_BUFFER]; + char jobid_out[DRMAA_JOBNAME_BUFFER]; + int status = 0; + drmaa_attr_values_t *rusage = NULL; + + errnum = drmaa_run_job (jobid, DRMAA_JOBNAME_BUFFER, jt, error, + DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not submit job: %s\n", error); + exception = 1; + } else { + printf ("Your job has been submitted with id %s\n", jobid); + + errnum = drmaa_wait (jobid, jobid_out, DRMAA_JOBNAME_BUFFER, &status, + DRMAA_TIMEOUT_WAIT_FOREVER, &rusage, error, + DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not wait for job: %s\n", error); + exception = 1; + } else { + char usage[DRMAA_ERROR_STRING_BUFFER]; + int aborted = 0; + + drmaa_wifaborted(&aborted, status, NULL, 0); + + if (aborted == 1) { + printf("Job %s never ran\n", jobid); + exception = 1; + } else { + int exited = 0; + + drmaa_wifexited(&exited, status, NULL, 0); + + if (exited == 1) { + int exit_status = 0; + + drmaa_wexitstatus(&exit_status, status, NULL, 0); + printf("Job %s finished regularly with exit status %d\n", jobid, exit_status); + exception = exit_status; + } else { + int signaled = 0; + + drmaa_wifsignaled(&signaled, status, NULL, 0); + + if (signaled == 1) { + char termsig[DRMAA_SIGNAL_BUFFER+1]; + + drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, status, NULL, 0); + printf("Job %s finished due to signal %s\n", jobid, termsig); + } else { + printf("Job %s finished with unclear conditions\n", jobid); + } + } /* else */ + } /* else */ + + printf ("Job Usage:\n"); + + while (drmaa_get_next_attr_value (rusage, usage, DRMAA_ERROR_STRING_BUFFER) == DRMAA_ERRNO_SUCCESS) { + printf (" %s\n", usage); + } + + drmaa_release_attr_values (rusage); + } /* else */ + } /* else */ + } /* else */ + + errnum = drmaa_delete_job_template (jt, error, DRMAA_ERROR_STRING_BUFFER); + + if (errnum != DRMAA_ERRNO_SUCCESS) { + fprintf (stderr, "Could not delete job template: %s\n", error); + } + } /* else */ + + return exception; + }|] + if e /= 0 then error ("status=" ++ show e) else return ()