Adjusting dim_t to make dimensions consistent

Question

Hello!

When trying to run my simulation, I obtain a line that says: "Adjusting dim_t to make dimensions consistent". I get no error but the simulation does not finish neither. What should I do? Do I have to do something to adjust the dimensions myself?

Thanks in advance!

Laura

Answer 1

Hi!

This message is from the IO routine. It means that the simulation lasted less than expected, which is exactly what you are experiencing. Could you please post the whole simulation output and also the parameters.par file from your simulation output directory? That way I get a better picture.

Comments

Hi!
Thanks for your answer. I cannot see any simulation output stored and I don't really get why. However, I copy here my .par file, hope it helps!

Also, I tried to run again the simulation in parallel and I get this message:
"[ec23975908f7:00037] Read -1, expected 183368, errno = 1
[ec23975908f7:00038] Read -1, expected 195936, errno = 1" again and again, it does not seem to stop.



# Parameter file
simID = /openCARP/atriaclara
vofile = vm_atria_regular
dt = 20
tend = 2500
meshname = /openCARP/atriaclara/atria
num_tsav = 1
tsav[0] = 2500
#tsav[1] = 3500
#write_statef =/openCARP/atriaclara/lv_ss_states

# IONIC SETUP
num_imp_regions = 9

# Right atrium and pectinate muscles
imp_region[0].name     = RA_PM
imp_region[0].num_IDs  = 7
imp_region[0].ID       = 32 34 74 104 193 195 199
imp_region[0].im       = JB_COURTEMANCHE
imp_region[0].im_param = "g_to=1.00,g_CaL=1.00,g_Kr=1.00"

# Crista terminalis and bachmann bundle right atrium
imp_region[1].name     = CT_BBRA
imp_region[1].num_IDs  = 2
imp_region[1].ID       = 72 102
imp_region[1].im       = JB_COURTEMANCHE
imp_region[1].im_param = "g_to=1.00,g_CaL=1.67,g_Kr=1.00"

# Tricuspid valve ring
imp_region[2].name     = TVR
imp_region[2].num_IDs  = 1
imp_region[2].ID       = 161
imp_region[2].im       = JB_COURTEMANCHE
imp_region[2].im_param = "g_to=1.00,g_CaL=0.67,g_Kr=1.53"

# Right atrial appendage
imp_region[3].name     = RAA
imp_region[3].num_IDs  = 1
imp_region[3].ID       = 111
imp_region[3].im       = JB_COURTEMANCHE
imp_region[3].im_param = "g_to=0.68,g_CaL=1.00,g_Kr=1.00"

# Left atrium
imp_region[4].name     = LA
imp_region[4].num_IDs  = 4
imp_region[4].ID       = 33 192 194 198
imp_region[4].im       = JB_COURTEMANCHE
imp_region[4].im_param = "g_to=1.00,g_CaL=1.00,g_Kr=1.60"

# Bachmann bundle left atrium
imp_region[5].name     = BBLA
imp_region[5].num_IDs  = 1
imp_region[5].ID       = 103
imp_region[5].im       = JB_COURTEMANCHE
imp_region[5].im_param = "g_to=1.00,g_CaL=1.67,g_Kr=1.60"

# Mitral valve ring
imp_region[6].name     = MVR
imp_region[6].num_IDs  = 1
imp_region[6].ID       = 162
imp_region[6].im       = JB_COURTEMANCHE
imp_region[6].im_param = "g_to=1.00,g_CaL=0.67,g_Kr=2.44"

# Left atrial appendage
imp_region[7].name     = LAA
imp_region[7].num_IDs  = 1
imp_region[7].ID       = 112
imp_region[7].im       = JB_COURTEMANCHE
imp_region[7].im_param = "g_to=0.68,g_CaL=1.00,g_Kr=1.60"

# Pulmonary valves
imp_region[8].name     = PV
imp_region[8].num_IDs  = 4
imp_region[8].ID       = 166 167 168 169
imp_region[8].im       = JB_COURTEMANCHE
imp_region[8].im_param = "g_to=1.00,g_CaL=1.00,g_Kr=2.20"


# CONDUCTIVITY VALUES/ TISSUE PROPERTIES
# Conductivity values: S/(m pF)
num_gregions = 9

# Right atrium
gregion[0].name    = RA
gregion[0].num_IDs = 4
gregion[0].ID      = 32 111 161 162
gregion[0].g_il    = 0,3
gregion[0].g_it    = 0,105    

# Crista Terminalis
gregion[1].name    = CT
gregion[1].num_IDs = 1
gregion[1].ID      = 72
gregion[1].g_il    = 0,85
gregion[1].g_it    = 0,1275

# Pulmonary valves
gregion[2].name    = PV
gregion[2].num_IDs = 4
gregion[2].ID      = 166 167 168 169
gregion[2].g_il    = 0,17
gregion[2].g_it    = 0,085

# Bachmann bundles and pectinate muscles
gregion[3].name    = BB_PM
gregion[3].num_IDs = 3
gregion[3].ID      = 74 102 103
gregion[3].g_il    = 0,75
gregion[3].g_it    = 0,1275

# Inferior isthmus
gregion[4].name    = II
gregion[4].num_IDs = 1
gregion[4].ID      = 104
gregion[4].g_il    = 0,15
gregion[4].g_it    = 0,15

# SA node
gregion[5].name    = SAN
gregion[5].num_IDs = 1
gregion[5].ID      = 34
gregion[5].g_il    = 0,08
gregion[5].g_it    = 0,08

# Coronary sinus
gregion[6].name    = CS
gregion[6].num_IDs = 2
gregion[6].ID      = 198 199
gregion[6].g_il    = 0,6
gregion[6].g_it    = 0,3

# Left atrium
gregion[7].name    = LA
gregion[7].num_IDs = 2
gregion[7].ID      = 33 112
gregion[7].g_il    = 0,3
gregion[7].g_it    = 0,105

# Anillo fossa ovalis
gregion[8].name    = AFO
gregion[8].num_IDs = 4
gregion[8].ID      = 192 193 194 195
gregion[8].g_il    = 0,75
gregion[8].g_it    = 0,1125


# STIMULUS SETUP
num_stim = 1

stimulus[0].start = 0          # ms
stimulus[0].strength = 2.2e1   # µA/cm* or mV
stimulus[0].duration = 2       # ms
stimulus[0].stimtype = 0       # [0-8]
stimulus[0].npls = 5           # dflt: 1
stimulus[0].bcl = 500         
stimulus[0].vtx_file =/openCARP/atriaclara/atria_SA_stim

#I/0 parameters
#timedt = 50
#spacedt = 5 #can increase to reduce data file size

#Meshname
meshname = /openCARP/atriaclara

#Matrix data
bidm_eqv_mono = 0
experiment = 0
mat_entries_per_row = 45
parab_solve = 1
cg_tol_ellip = 1e-4
bidomain = 0

Thanks you!

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Regarding your error messages: Those look like an MPI issue to me.

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Hi! How was this eventually solved? I have this line 4 times in a row and then the simulations does start running. However, I don't get what parameter was set to a wrong value.

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This are not openCARP error messages. I suspect they come from MPI.

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Hi Aurel,

Sorry to bring this up again, but do you know if there are any fixes for this? I am running openCARP via carputils, and receive this message whether I use job.carp or job.mpi.

Thanks
Sam

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Hi!

No, I see no reason for this to slow down your simulations.

The message just means that when initially generating the igb file, dim_t was expected to be of one size, but then later turned out to be of another size. For example this can happen when restarting, but also when aborting a simulation.

The initial post in this thread described some form of simulation abort, as there were not enough time steps outputted.

If in your situation everything behaves as expected, then there is no problem.

Best, Aurel

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Thanks Aurel, I think that I was just receiving this error message at a point where the code was doing some other work that didn't have terminal output.