Relion/qsub

--- relion/src/gui_jobwindow.cpp.orig   2019-02-26 21:02:00.360382892 +0900
+++ relion/src/gui_jobwindow.cpp        2019-02-27 00:03:33.152566319 +0900
@@ -218,6 +218,7 @@
 
        if (myjob.joboptions.find("nr_mpi") != myjob.joboptions.end())
        {
+               if (myjob.joboptions.find("nr_nodes") != myjob.joboptions.end()) place("nr_nodes", TOGGLE_LEAVE_ACTIVE);
                place("nr_mpi", TOGGLE_LEAVE_ACTIVE);
                has_parallel = true;
        }
@@ -259,11 +260,6 @@
 
        place("qsubscript");
 
-       place("min_dedicated");
-       if (do_allow_change_minimum_dedicated)
-               guientries["min_dedicated"].deactivate(false);
-       else
-               guientries["min_dedicated"].deactivate(true);
 
        queue_group->end();
        guientries["do_queue"].cb_menu_i(); // This is to make the default effective

--- relion/src/pipeline_jobs.cpp.orig   2019-02-26 21:02:00.417383141 +0900
+++ relion/src/pipeline_jobs.cpp        2019-02-27 00:12:56.481952706 +0900
@@ -433,25 +433,18 @@
                int nmpi = (joboptions.find("nr_mpi") != joboptions.end()) ? joboptions["nr_mpi"].getNumber() : 1;
                int nthr = (joboptions.find("nr_threads") != joboptions.end()) ? joboptions["nr_threads"].getNumber() : 1;
                int ncores = nmpi * nthr;
-               int ndedi = joboptions["min_dedicated"].getNumber();
-               float fnodes = (float)ncores / (float)ndedi;
-               int nnodes = CEIL(fnodes);
-               if (fmod(fnodes, 1) > 0)
-               {
-                       std:: cout << std::endl;
-                       std::cout << " Warning! You're using " << nmpi << " MPI processes with "(略
-                       std::cout << " It is more efficient to make the number of cores (i.e. mpi*threads)(略
-               }
 
                fh.clear(); // reset eof if happened...
                fh.seekg(0, std::ios::beg);
                std::string line;
                std::map<std::string, std::string> replacing;
+               replacing["XXXversionXXX"] = RELION_VERSION;
+               replacing["XXXsumXXX"] = floatToString( joboptions["nr_nodes"].getNumber() * ncores );
+               replacing["XXXmpiprocXXX"] = floatToString( joboptions["nr_nodes"].getNumber() * nmpi );
                replacing["XXXmpinodesXXX"] = floatToString(nmpi);
                replacing["XXXthreadsXXX"] = floatToString(nthr);
                replacing["XXXcoresXXX"] = floatToString(ncores);
-               replacing["XXXdedicatedXXX"] = floatToString(ndedi);
-               replacing["XXXnodesXXX"] = floatToString(nnodes);
+               replacing["XXXnodesXXX"] = floatToString( joboptions["nr_nodes"].getNumber() );
                replacing["XXXnameXXX"] = outputname;
                replacing["XXXerrfileXXX"] = outputname + "run.err";
                replacing["XXXoutfileXXX"] = outputname + "run.out";
@@ -755,7 +748,8 @@
        const char qsub_nrmpi_val = (qsub_nrmpi_text ? atoi(qsub_nrmpi_text) : DEFAULTNRMPI);
        if (has_mpi)
        {
-               joboptions["nr_mpi"] = JobOption("Number of MPI procs:", qsub_nrmpi_val , 1, mpi_max, 1,(略
+               joboptions["nr_mpi"] = JobOption("Number of MPI procs per node:", qsub_nrmpi_val , 1, (略
+               joboptions["nr_nodes"] = JobOption("Number of nodes:", 1, 1, 8 , 1, "Number of nodes");
        }
 
        const char *thread_max_input = getenv("RELION_THREAD_MAX");
@@ -835,11 +829,12 @@
 In the template script a number of variables will be replaced: \n \
 XXXcommandXXX = relion command + arguments; \n \
 XXXqueueXXX = The queue name; \n \
-XXXmpinodesXXX = The number of MPI nodes; \n \
-XXXthreadsXXX = The number of threads; \n \
+XXXmpinodesXXX = The number of MPI per node; \n \
+XXXmpiprocXXX = The total number of MPI; \n \
+XXXthreadsXXX = The number of threads per MPI; \n \
 XXXcoresXXX = XXXmpinodesXXX * XXXthreadsXXX; \n \
-XXXdedicatedXXX = The minimum number of dedicated cores on each node; \n \
-XXXnodesXXX = The number of requested nodes = CEIL(XXXcoresXXX / XXXdedicatedXXX); \n \
+XXXsumXXX = The total number of core; \n \
+XXXnodesXXX = The number of requested nodes \n \
 If these options are not enough for your standard jobs, you may define a user-specified number of extra(略
 The number of extra variables is controlled through the environment variable RELION_QSUB_EXTRA_COUNT. \
 Their help text is set by the environment variables RELION_QSUB_EXTRA1, RELION_QSUB_EXTRA2, etc \
@@ -849,9 +844,6 @@
 But note that (unlike all other entries in the GUI) the extra values are not remembered from one run to the other.");
 
        // Check for environment variable RELION_QSUB_TEMPLATE
-       char * my_minimum_dedicated = getenv ("RELION_MINIMUM_DEDICATED");
-       int minimum_nr_dedicated = (my_minimum_dedicated == NULL) ? DEFAULTMININIMUMDEDICATED : (略
-       joboptions["min_dedicated"] = JobOption("Minimum dedicated cores per node:", minimum_nr_dedicated, (略
 
        // Need the std::string(), as otherwise it will be overloaded and passed as a boolean....
        joboptions["other_args"] = JobOption("Additional arguments:", std::string(""), "In this box (略

[root@c ~]# vi /Appl/src/relion/src/apps/maingui.cpp
 :
 #ifdef PACKAGE_VERSION
         strcat(titletext,PACKAGE_VERSION);
 #endif
-        strcat(titletext,": ");
+        strcat(titletext,": 190226, cuda-10.2 :");
 
        strcat (titletext, short_dir);
 :
[root@c ~]#