adaptivecomputationlab / simcov Goto Github PK

What should the infection-coords parameter be set to when the infections parameter is greater than 1? Or is this parameter irrelevant when the number of infections is greater than 1?

I encountered this error on Xena at CARC in the slurm output file.

My run still completed, but I did not get the typical output message about how long it took and such.

[12/01/20 09:54:13 696.84s]: 39494 337944 451219 64110 19994688 1832 14437 1.74e-03 1.83e+01 < 0.699 0.789 >
[12/01/20 10:05:46 693.64s]: 40300 343744 457149 67264 20772526 1748 14488 1.77e-03 1.87e+01 < 0.711 0.805 >
[12/01/20 10:06:02 15.73s]: 40319 343835 457395 67065 20791232 1730 14476 1.77e-03 1.87e+01 < 0.712 0.806 >
/var/spool/slurm/d/job08214/slurm_script: line 12: 9606 Bus error upcxx-run -n $SLURM_NTASKS -N $SLURM_NNODES -- ./install/bin/simcov --config configs/ode_run_1_foi_2_inf_coords.config

Might be connected to #7?

I recall that you mentioned to guarantee an infection at a single location in round 0, the initial-infection and infectivity multiplied should be at least 1: initial-infection * infectivity = 1.

Does this initial-infection need to scaled by the number of infections if you want to guarantee an infection at multiple locations?

Chemokine is a proxy of the spread of an infection, so we need to know how many cells have chemokine. Add a final column to the simcov.stats with this number.

The generation rate should still be the same as for the whole lung, but have the probability of extravasation should be dependent on the subset of the lung simulated, eg if we are simulating 0.1 of the lung, then the probability of extravasation where the chemokine is should be 0.1.

I've tracked down why sometimes on various systems SIMCoV can give the warning: "Could not pin process x to core y." If I request a resource allocation where I get cores, for example, 50-57 and run an 8 process job, the pin_thread function in src/utils.cpp will fail and return a warning because it will try to pin the processes to cores 0-7. Not sure at this moment how to check which cores a slurm like job scheduler gives you at run time.

Currently, we record every single grid point in the sample file (or an average of subsets of points when subsampling). But it's highly likely that in a lot of runs the data of interest will be sparse (concentrated around a few points of infection) and so most of the data written will be unnecessary. We should change to only subsample the active areas. This may be best to do in conjunction with using the modern vtk format.

Hello!

I got an error when I set the sample period for one of my runs running on 14 nodes on Xena at CARC.

Here is the script that I submitted:

#!/bin/bash
#SBATCH --partition=singleGPU
#SBATCH --nodes=14
#SBATCH --ntasks-per-node=16
#SBATCH --time=2-00:00:00
#SBATCH --job-name=simcov_test
#SBATCh --output=simcov.out

module load upcxx/2020.10.0-python3-3o75
module load cmake/3.18.4-2lmi

upcxx-run -n $SLURM_NTASKS -N $SLURM_NNODES -- ./install/bin/simcov --config=../simcov-results/configs/tcl_configs/ode_run_tcl_config/ode_run_tcl_20000_foi_600.config --sample-period 1440

The slurm.out file is VERY long, so I put it in this Google Drive folder: https://drive.google.com/drive/folders/16XnZj9sce_Cy5aqJ9MyzXgETjuNOnJdW?usp=sharing

Here is what is in the different files in the simcov-run-n... directory that was generated:

simcov.stats

time incb expr apop dead tvas ttis chem virs

simcov.log

2020-12-16 18:10:30 SimCov version SimCov version 0.1.1.cc7f682-dirty-master built on 20201215_121229
2020-12-16 18:10:30 _________________________
2020-12-16 18:10:30 Compiler definitions:
2020-12-16 18:10:30 _XOPEN_SOURCE=700
2020-12-16 18:10:30 CONFIG_USE_COLORS
2020-12-16 18:10:30 USE_BYTELL
2020-12-16 18:10:30 MAX_VIRIONS=125000
2020-12-16 18:10:30 _________________________
2020-12-16 18:10:30 Options:
2020-12-16 18:10:30 dim = 20000 20000 1
2020-12-16 18:10:30 timesteps = 20160
2020-12-16 18:10:30 infections = 600
2020-12-16 18:10:30 infection-coords = []
2020-12-16 18:10:30 initial-infection = 300000
2020-12-16 18:10:30 infectable-spacing = 1
2020-12-16 18:10:30 incubation-period = 360
2020-12-16 18:10:30 apoptosis-period = 180
2020-12-16 18:10:30 expressing-period = 2057
2020-12-16 18:10:30 infectivity = 0.00247
2020-12-16 18:10:30 virion-production = 35
2020-12-16 18:10:30 virion-decay = 0.0069
2020-12-16 18:10:30 virion-diffusion = 1
2020-12-16 18:10:30 chemokine-production = 0.5
2020-12-16 18:10:30 chemokine-decay = 0.02
2020-12-16 18:10:30 chemokine-diffusion = 0.5
2020-12-16 18:10:30 min-chemokine = 1e-6
2020-12-16 18:10:30 antibody-factor = 1
2020-12-16 18:10:30 antibody-period = 5760
2020-12-16 18:10:30 tcell-generation-rate = 10
2020-12-16 18:10:30 tcell-initial-delay = 20160
2020-12-16 18:10:30 tcell-vascular-period = 5760
2020-12-16 18:10:30 tcell-tissue-period = 1440
2020-12-16 18:10:30 tcell-binding-period = 10
2020-12-16 18:10:30 max-binding-prob = 1
2020-12-16 18:10:30 tcells-follow-gradient = false
2020-12-16 18:10:30 seed = 29
2020-12-16 18:10:30 sample-period = 1440
2020-12-16 18:10:30 sample-resolution = 1
2020-12-16 18:10:30 min-blocks-per-proc = 16
2020-12-16 18:10:30 output = simcov-run-n224-N14-201216181030
2020-12-16 18:10:30 _________________________
2020-12-16 18:10:30 Starting run with 224 processes on 14 nodes at 12/16/20 18:10:30
2020-12-16 18:10:30 Pinned processes, with process 0 (pid 3964) pinned to core 0
2020-12-16 18:10:30 Initial free memory across all nodes: 826.18GB
2020-12-16 18:10:30 Starting with 59.00GB free on node 0
2020-12-16 18:10:30 Dividing 400000000 grid points into 6400 squares of size 62500 (250^2), with 29 per process
2020-12-16 18:10:30 Total initial memory required per process is a max of 165.94MB
2020-12-16 18:10:34 --- Elapsed time for tissue.cpp:Tissue: (exiting barrier) 2020-12-16 18:10:34 ...
2020-12-16 18:10:34 ... (min/my/avg/max, bal) (3.60/3.60/3.60/3.60 s, 1.00) barrier(0.00 s) ---
2020-12-16 18:10:34 Memory used on node 0 after initialization is 9.15GB
2020-12-16 18:10:34 ... (min/my/avg/max, bal) No-Time barrier(0.00 s) ---
2020-12-16 18:10:34 # datetime elapsed step incb expr apop dead tvas ttis chem virs <%active lbln>
2020-12-16 18:10:34 Time step 0: initial infection at (13164, 15138, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7466, 1517, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8279, 9922, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18287, 353, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1056, 18379, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3445, 178, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17843, 11989, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4336, 11898, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15944, 15380, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16723, 14120, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3591, 979, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4219, 3463, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12721, 19866, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12424, 18047, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19321, 11421, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16088, 13182, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2895, 2028, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2927, 15591, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7639, 8537, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14203, 7701, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2546, 583, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4866, 6247, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6251, 11004, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2712, 3691, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5398, 650, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7815, 3841, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11180, 3622, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19529, 17890, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16820, 1658, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10619, 12186, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15150, 18572, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5744, 16552, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12026, 17102, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6174, 11242, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10894, 4357, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14836, 9600, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10563, 12001, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3208, 10514, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1351, 5985, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17823, 10198, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2572, 18386, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6125, 6544, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18133, 13571, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17695, 1673, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9263, 3659, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10749, 417, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (563, 18901, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10211, 15130, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14716, 2372, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15647, 18323, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9484, 668, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19391, 12659, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18541, 1281, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12517, 4356, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5683, 4767, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11990, 17515, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13218, 19832, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14752, 19339, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5903, 359, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (918, 7280, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9669, 4767, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6804, 17203, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12451, 19913, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (48, 5501, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6845, 6982, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (708, 8682, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14290, 8932, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17947, 19100, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13667, 9703, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13616, 13773, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12555, 13413, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1783, 3973, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1802, 16324, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16707, 5007, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (507, 13773, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10331, 3325, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11420, 4077, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7540, 10016, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10137, 19169, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12465, 14600, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13573, 6079, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6818, 7022, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9884, 10121, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12936, 4769, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19987, 15346, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (315, 5674, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14180, 1483, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12296, 7663, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15194, 229, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4051, 17493, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14588, 15725, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (603, 9374, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (819, 9033, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6825, 8930, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13342, 12699, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12277, 16456, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5919, 13514, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9849, 5306, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7905, 11143, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9639, 10027, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (613, 5869, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16604, 17093, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13537, 6136, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2236, 5070, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4554, 14752, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8482, 3395, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (294, 5124, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2083, 11848, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4000, 6176, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10301, 12362, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6036, 13877, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1585, 5035, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8930, 15125, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12646, 13071, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2607, 17004, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8576, 13926, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16425, 15934, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6004, 6670, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16780, 1294, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5037, 12029, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14917, 14136, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7888, 18733, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5341, 18165, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14253, 3692, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18001, 5162, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3623, 4874, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19085, 7956, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5098, 1479, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (996, 19632, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5689, 9577, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16061, 11187, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5757, 15225, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7958, 2275, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17965, 2373, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12981, 16099, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5398, 16293, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12435, 7956, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16642, 6020, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18215, 4664, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16884, 16756, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14423, 14112, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1273, 14531, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19708, 9442, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14703, 19689, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14368, 1546, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2466, 7757, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16583, 1286, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11473, 16589, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5482, 10720, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6351, 5836, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12045, 2030, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7445, 3534, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14706, 7688, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (348, 8139, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18124, 7686, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18112, 6069, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15000, 12850, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8731, 16066, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19920, 19377, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16017, 8425, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17289, 16332, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16949, 13541, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11586, 7881, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19484, 1487, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15429, 10674, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2470, 18996, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5175, 17153, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19237, 16445, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13136, 11921, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2798, 5181, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10346, 4716, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18255, 13276, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4275, 5111, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1774, 11106, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14879, 15476, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5683, 16734, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12343, 1359, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15241, 6005, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3483, 13101, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8826, 16680, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18026, 17863, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4185, 11075, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2410, 13875, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15178, 5137, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3703, 17113, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14681, 16020, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10357, 1521, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19706, 16839, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12975, 4729, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19673, 12893, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2696, 13279, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (954, 10290, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (840, 4714, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8408, 9535, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8016, 9580, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15558, 16656, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12879, 10197, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7608, 13137, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15622, 13455, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3234, 163, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12043, 19833, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1636, 17293, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2981, 1057, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6515, 10085, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18587, 19740, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5958, 8593, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7504, 10754, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11051, 16326, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6417, 16980, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16990, 2563, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9813, 5043, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10731, 14625, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10210, 11952, 0)
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2020-12-16 18:10:34 Time step 0: initial infection at (8881, 15040, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1734, 10044, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16268, 3745, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1559, 16963, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11720, 18677, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18290, 5610, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18205, 2200, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5705, 4206, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3840, 5455, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5988, 15659, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8318, 14992, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17100, 6898, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14974, 15784, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12397, 14457, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1303, 11940, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3263, 13931, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (135, 6536, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3062, 10705, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14780, 8262, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4685, 5313, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18230, 2162, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5960, 4302, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7837, 9317, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5281, 9305, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5951, 10852, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15233, 18531, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4822, 12146, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19978, 11352, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17458, 5923, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15795, 16362, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1552, 4980, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6899, 9968, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (636, 13539, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9280, 13891, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14502, 8447, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11813, 15701, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6687, 12893, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12366, 3591, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16225, 9410, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (583, 14131, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17524, 16699, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9476, 3211, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (16066, 10100, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18935, 5904, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18194, 18373, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (725, 10999, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15702, 1087, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19625, 17926, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15236, 4735, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14083, 17776, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17580, 6632, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15007, 4, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9617, 12795, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6825, 19911, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (4809, 5249, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15653, 7400, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10536, 7859, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3893, 7168, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3118, 2137, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9013, 17619, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11622, 6655, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (10834, 8953, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (5151, 5444, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8489, 4118, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (12894, 2376, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6257, 18960, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (9756, 18877, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (999, 10537, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14885, 10734, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14895, 5252, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14300, 13451, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18250, 3419, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11734, 5904, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11003, 8154, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19935, 15803, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (6037, 2420, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3400, 18995, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (15978, 1986, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3242, 7922, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (276, 11801, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18816, 14968, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (18300, 9682, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (3526, 14705, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2568, 16926, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (17199, 16419, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13105, 1054, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (14270, 15453, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1925, 17480, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7327, 7486, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (2626, 12184, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (19161, 2333, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7338, 19239, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8593, 15295, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (1958, 14054, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (13814, 12671, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (11241, 6919, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (8359, 398, 0)
2020-12-16 18:10:34 Time step 0: initial infection at (7191, 17839, 0)
2020-12-16 18:10:34 [12/16/20 18:10:34 0.02s]: 0 600 0 0 0 0 0 0.00e+00 0.00e+00 < 0.000 0.383 >

samples directory

[apribis@xena simcov-run-n224-N14-201216181030]$ cd samples/
[apribis@xena samples]$ ls
sample_epicell_0.vtk

Thanks!

Only log and stats files written, nothing put in samples folder

I encountered this warning in the generated slurm.out file when running with 3 nodes on CARC Xena.

WARNING: ./install/bin/simcov was compiled with smp backend, which only supports single-node operation. -N option ignored.
WARNING: For multi-node operation, please re-compile with UPCXX_NETWORK=<backend>
Initial infection coordinates set; will override --infections (1)
Initial infection coords specified, setting number of infection points to 1

And after printing out the config:

Starting run with 48 processes on 1 node at 11/29/20 21:20:55
[39] <main.cpp:641> WARNING: Could not pin process 29783 to core 39
[17] <main.cpp:641> WARNING: Could not pin process 29761 to core 17
[33] <main.cpp:641> WARNING: Could not pin process 29777 to core 33
[21] <main.cpp:641> WARNING: Could not pin process 29765 to core 21
[44] <main.cpp:641> WARNING: Could not pin process 29788 to core 44
[43] <main.cpp:641> WARNING: Could not pin process 29787 to core 43
[18] <main.cpp:641> WARNING: Could not pin process 29762 to core 18
[29] <main.cpp:641> WARNING: Could not pin process 29773 to core 29
[25] <main.cpp:641> WARNING: Could not pin process 29769 to core 25
[24] <main.cpp:641> WARNING: Could not pin process 29768 to core 24
[42] <main.cpp:641> WARNING: Could not pin process 29786 to core 42
[16] <main.cpp:641> WARNING: Could not pin process 29760 to core 16
[22] <main.cpp:641> WARNING: Could not pin process 29766 to core 22
[45] <main.cpp:641> WARNING: Could not pin process 29789 to core 45
[36] <main.cpp:641> WARNING: Could not pin process 29780 to core 36
[34] <main.cpp:641> WARNING: Could not pin process 29778 to core 34
[32] <main.cpp:641> WARNING: Could not pin process 29776 to core 32
[38] <main.cpp:641> WARNING: Could not pin process 29782 to core 38
[23] <main.cpp:641> WARNING: Could not pin process 29767 to core 23
[35] <main.cpp:641> WARNING: Could not pin process 29779 to core 35
[41] <main.cpp:641> WARNING: Could not pin process 29785 to core 41
[26] <main.cpp:641> WARNING: Could not pin process 29770 to core 26
[30] <main.cpp:641> WARNING: Could not pin process 29774 to core 30
[37] <main.cpp:641> WARNING: Could not pin process 29781 to core 37
[40] <main.cpp:641> WARNING: Could not pin process 29784 to core 40
[46] <main.cpp:641> WARNING: Could not pin process 29790 to core 46
[19] <main.cpp:641> WARNING: Could not pin process 29763 to core 19
[20] <main.cpp:641> WARNING: Could not pin process 29764 to core 20
[27] <main.cpp:641> WARNING: Could not pin process 29771 to core 27
[28] <main.cpp:641> WARNING: Could not pin process 29772 to core 28
[31] <main.cpp:641> WARNING: Could not pin process 29775 to core 31
[47] <main.cpp:641> WARNING: Could not pin process 29791 to core 47

This is the only thing I have changed from running with a single node to three nodes:

In the xena_simcov_run.sh script:
#SBATCH --nodes=3
INSTEAD OF:
#SBATCH --nodes=1

Is this something I need to worry about?

Sorry for all the questions...

While trying to visualize things in paraview, I realized that my samples directory in my run is empty.

Here is a folder with my log file, config file, stats file, and slurm output file: https://drive.google.com/drive/folders/1mCCvyrbsWAYaisKt59cO2zebUTpMPLvr

I have tried rebuilding SIMCoV, but I still get an empty samples directory.

Let me know if any other information would be useful!

I got the following error when trying to run simcov. I have a feeling that it is a CARC problem, so I will open a ticket with them on Monday, but I just wanted to check here too and make the issue known:

First, I made sure that my local directory matched this directory:

[apribis@xena simcov]$ git status
On branch master
nothing to commit, working directory clean

Then, I ran the default Xena script in batch-scripts/carc/xena_simcov_run.sh, and I got this error:

You have not been allocated GPUs. To request GPUs, add the following to your submission script (where X is the number of GPUs to request): #SBATCH --gres=gpu:X

Error: "./install/bin/simcov" does not appear to execute a UPC++/GASNet executable
usage: upcxx-run [-h] [-n NUM] [-N NUM] [-shared-heap HEAPSZ] [-backtrace]
[-show] [-info] [-ssh-servers HOSTS] [-localhost] [-v]
[-E VAR1[,VAR2]]
command ...

This seems to indicate the script must be modified to allocate GPUs, but the error below looks like UPC++ was not installed correctly. Therefore, I tried rebuilding:

[apribis@xena simcov]$ module load upcxx/2020.10.0-python3-3o75

The following have been reloaded with a version change:

1. zlib/1.2.11-pkmj => zlib/1.2.11-lfst

[apribis@xena simcov]$ ./build.sh Release
./build.sh: line 41: cmake: command not found
[apribis@xena simcov]$ module load cmake/3.18.4-2lmi
[apribis@xena simcov]$ ./build.sh Release
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Building Release version
-- Submodule update of upcxx-utils
-- 37018525d0c4a97650fe01947de1d9fe4dd99499 upcxx-utils (v0.3.0-29-g3701852) matched '^ .* upcxx-utils'
-- SIMCOV base version 0.1.1 (0.1.1)
-- SIMCOV_BUILD_DATE=20201211_184439
-- No external upcxx-utils package provided
-- CMAKE_MODULE_PATH: /users/apribis/simcov/cmake/Modules
-- Did not find an installation of upcxx_utils, including submodule in src/upcxx_utils
-- Building for Release
-- UPCXX_UTILS base version 0.3.0 (0.3.0)
-- UPCXX_UTILS_BUILD_DATE=20201211_184439
-- Testing the environment..
-- Found UPCXX: /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/bin/upcxx-meta
-- Found UPCXX: /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/bin/upcxx-meta
CMake Warning at /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/share/cmake/UPCXX/UPCXXConfig.cmake:129 (message):
Compiler compatibility check failed!

UPCXX compiler provided by upcxx-meta CXX:

  /opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx ->
  /opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx

is different from CMAKE_CXX_COMPILER:

  /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++ ->
  /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++

Please either pass cmake:
-DCMAKE_CXX_COMPILER=/opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx

or re-install UPC++ with:
CXX=/opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++

Call Stack (most recent call first):
upcxx-utils/CMakeLists.txt:76 (find_package)

-- Could NOT find UPCXX (missing: UPCXX_COMPATIBLE_COMPILER) (found version "2020.10.0")
-- This UPC++ install requires the c++11 standard.
-- UPCXX_NETWORK=smp
-- UPCXX_THREADMODE=seq
-- UPCXX_CODEMODE=O3
CMake Warning at upcxx-utils/CMakeLists.txt:76 (find_package):
Found package configuration file:

/opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/share/cmake/UPCXX/UPCXXConfig.cmake

but it set UPCXX_FOUND to FALSE so package "UPCXX" is considered to be NOT
FOUND.

-- Using UPCXX version - 2020.10.0 20201000
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- UPCXX_UTILS is using the UPCXX::upcxx library interface: -L/opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/upcxx.opt.gasnet_seq.smp/lib -lupcxx -L/opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/gasnet.opt/lib -lgasnet-smp-seq -lrt -L/opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/lib/gcc/x86_64-pc-linux-gnu/10.2.0 -lgcc -lm
-- Found UPCXX: /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/bin/upcxx-meta
-- Found UPCXX: /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/bin/upcxx-meta
CMake Warning at /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/share/cmake/UPCXX/UPCXXConfig.cmake:129 (message):
Compiler compatibility check failed!

UPCXX compiler provided by upcxx-meta CXX:

  /opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx ->
  /opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx

is different from CMAKE_CXX_COMPILER:

  /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++ ->
  /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++

Please either pass cmake:
-DCMAKE_CXX_COMPILER=/opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx

or re-install UPC++ with:
CXX=/opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++

Call Stack (most recent call first):
upcxx-utils/test/CMakeLists.txt:2 (find_package)

-- Could NOT find UPCXX (missing: UPCXX_COMPATIBLE_COMPILER) (found version "2020.10.0")
-- This UPC++ install requires the c++11 standard.
-- UPCXX_NETWORK=smp
-- UPCXX_THREADMODE=seq
-- UPCXX_CODEMODE=O3
CMake Warning at upcxx-utils/test/CMakeLists.txt:2 (find_package):
Found package configuration file:

/opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/share/cmake/UPCXX/UPCXXConfig.cmake

but it set UPCXX_FOUND to FALSE so package "UPCXX" is considered to be NOT
FOUND.

-- Installing package version 0.3.0
-- UPCXX_UTILS-utils build type: Release
-- added upcxx_utils ()
-- finding UPCXX for SimCov build
-- Found UPCXX: /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/bin/upcxx-meta
-- Found UPCXX: /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/bin/upcxx-meta
CMake Warning at /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/share/cmake/UPCXX/UPCXXConfig.cmake:129 (message):
Compiler compatibility check failed!

UPCXX compiler provided by upcxx-meta CXX:

  /opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx ->
  /opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx

is different from CMAKE_CXX_COMPILER:

  /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++ ->
  /opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++

Please either pass cmake:
-DCMAKE_CXX_COMPILER=/opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpicxx

or re-install UPC++ with:
CXX=/opt/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gcc-10.2.0-3kjqvw7masskmxqtxblo5khyshwe6zuw/bin/g++

Call Stack (most recent call first):
src/CMakeLists.txt:5 (find_package)

CMake Error at /opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/cmake-3.18.4-2lmiaz6aejwfswraarbhj37mdvspumnw/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:165 (message):
Could NOT find UPCXX (missing: UPCXX_COMPATIBLE_COMPILER) (found version
"2020.10.0")
Call Stack (most recent call first):
/opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/cmake-3.18.4-2lmiaz6aejwfswraarbhj37mdvspumnw/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:458 (_FPHSA_FAILURE_MESSAGE)
/opt/spack/opt/spack/linux-centos7-haswell/gcc-10.2.0/upcxx-2020.10.0-3o75bajpdualqb5h57uhpcsnccnf3bf5/share/cmake/UPCXX/UPCXXConfig.cmake:269 (find_package_handle_standard_args)
src/CMakeLists.txt:5 (find_package)

-- Configuring incomplete, errors occurred!
See also "/users/apribis/simcov/.build/CMakeFiles/CMakeOutput.log".
See also "/users/apribis/simcov/.build/CMakeFiles/CMakeError.log".

I put the two log files ( /users/apribis/simcov/.build/CMakeFiles/CMakeOutput.log and /users/apribis/simcov/.build/CMakeFiles/CMakeError.log) in this directory: https://drive.google.com/drive/folders/1wVpO435f6r1QnqI-wUUrZ2y0zLsDMbR0?usp=sharing

Add multipliers [0.0, 1.0] to virus production and infectivity parameters that permit the modelling of local effects of interferon.

Not all epicells are infectable. Within the alveoli, only the type II pneumocytes are, and they constitute about 60% of the cells, but are fairly widely spaced. They surround the much bigger type II's and are probably at least 15 microns apart. They are themselves 9 microns across. Within the bronchioles, only the club cells are infectable. We need to reflect that in the model. I think this means that grid points should be 9 or 10 microns apart, because we have no mechanism of representing an epicell spanning multiple grid points. I also think we'll need to have epicells marked as either infectable or invulnerable, because we don't want empty air (null ptrs for epicells) when there are actually cells there, because T cells don't move through empty spaces, so it would block their progress. Presumably we can incorporate these strictures into the structure/network generation code.

Hello!

I was a little confused about how to visualize the samples directory in paraview.

Here are my questions:

1. I know the README mentions using the sample-state.py file to generate a paraview state file. Has this been replaced by the generate_paraview_state.py file in the scripts directory?
2. I should be able to run paraview on the CARC machines, so I don't need to install paraview on my computer, correct?
   a. If I can run it at CARC, which paraview version should I module load in the compute node?
   b. If I need to install it on my computer, could I please get a link to the recommended installation instructions?
3. Is pvpython a different installation (or module load) in addition to paraview?

Thanks!

Currently, tcells start being produced after options.tcell_initial_delay, and the production is ramped up linearly over a period of half of that, i.e. tcell production finally reaches options.tcell_generation_rate after 1.5*options.tcell_initial_delay. Is this realistic? Or is it a good enough approximation to have no linear ramp up, and just switch the tcells on. Even without the ramp up, if we observe the tcell count in the vasculature, it will grow linearly until it reaches a steady state level (in the absence of any virus causing extravasation). This appears to be what it looks like in data on tcell levels in patients, so it may be a good enough approximation.

Currently the T cells in a location are stored in a vector, and there is no limit to how many can be in one place. But this is unrealistic as T cells take up space and so there should be a limit on this vector.

The two parameters for setting the initial infections, --infections and --infection-coords overlap in non-obvious ways. Change this by removing --infections and allow --infection-coords to specify something like --infection-coords=random5 for 5 locations, or any other initial number.

Write a python wrapper script that calls upcxx-run and sets up all the necessary variables, etc, and stripes the output directory (on Cori), etc.

Mod simcov to accept the latest branching airways model output "airways.dat" file format.

The following variables set in simcov/slurm_hopper.sh are already set by the upcxx module. If we upgrade or replace that module these exports will cause simcov to fail. Please remove these lines from the script. Thanks.

export UPCXX=/opt/spack/opt/spack/linux-rocky8-cascadelake/gcc-12.1.0/upcxx-2020.10.0-6eh2prmiaolqfqinq4wjbb5by6z2phw6/bin/upcxx
export UPCXX_BIN=/opt/spack/opt/spack/linux-rocky8-cascadelake/gcc-12.1.0/upcxx-2020.10.0-6eh2prmiaolqfqinq4wjbb5by6z2phw6/bin
export UPCXX_INC=/opt/spack/opt/spack/linux-rocky8-cascadelake/gcc-12.1.0/upcxx-2020.10.0-6eh2prmiaolqfqinq4wjbb5by6z2phw6/include
export UPCXX_INSTALL=/opt/spack/opt/spack/linux-rocky8-cascadelake/gcc-12.1.0/upcxx-2020.10.0-6eh2prmiaolqfqinq4wjbb5by6z2phw6
export UPCXX_LIB=/opt/spack/opt/spack/linux-rocky8-cascadelake/gcc-12.1.0/upcxx-2020.10.0-6eh2prmiaolqfqinq4wjbb5by6z2phw6/lib
export UPCXX_ROOT=/opt/spack/opt/spack/linux-rocky8-cascadelake/gcc-12.1.0/upcxx-2020.10.0-6eh2prmiaolqfqinq4wjbb5by6z2phw6