Message-Passing-Interface MPI Parallelization of Iteratively Coupled Fluid Flow and Geomechanics Codes for the Simulation of System Behavior in Hydrate-Bearing Geologic Media

2021 ◽  
Author(s):  
Jiecheng Zhang ◽  
George Moridis ◽  
Thomas Blasingame
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Gas Production ◽  
Parallel Performance ◽  
Group 3 ◽  
Linux Cluster ◽  
Group 2 ◽  
3D Problem ◽  
Group 1

Abstract The Reservoir GeoMechanics Simulator (RGMS), a geomechanics simulator based on the finite element method and parallelized using the Message Passing Interface (MPI), is developed in this work to model the stresses and deformations in subsurface systems. RGMS can be used stand-alone, or coupled with flow and transport models. pT+H V1.5, a parallel MPI-based version of the serial T+H V1.5 code that describes mass and heat flow in hydrate-bearing porous media, is also developed. Using the fixed-stress split iterative scheme, RGMS is coupled with the pT+H V1.5 to investigate the geomechanical responses associated with gas production from hydrate accumulations. The code development and testing process involve evaluation of the parallelization and of the coupling method, as well as verification and validation of the results. The parallel performance of the codes is tested on the Ada Linux cluster of the Texas A&M High Performance Research Computing using up to 512 processors, and on a Mac Pro computer with 12 processors. The investigated problems are: Group 1: Geomechanical problems solved by RGMS in 2D Cartesian and cylindrical domains and a 3D problem, involving 4x106 and 3.375 x106 elements, respectively; Group 2: Realistic problems of gas production from hydrates using pT+H V1.5 in 2D and 3D systems with 2.45x105 and 3.6 x106 elements, respectively; Group 3: The 3D problem in Group 2 solved with the coupled RGMS-pT+H V1.5 simulator, fully accounting for geomechanics. Two domain partitioning options are investigated on the Ada Linux cluster and the Mac Pro, and the code parallel performance is monitored. On the Ada Linux cluster using 512 processors, the simulation speedups (a) of RGMS are 218.89, 188.13, and 284.70 in the Group 1 problems, (b) of pT+H V1.5 are 174.25 and 341.67 in the Group 2 cases, and (c) of the coupled simulators is 331.80 in Group 3. The results produced in this work show the necessity of using full geomechanics simulators in marine hydrate-related studies because of the associated pronounced geomechanical effects on production and displacements and (b) the effectiveness of the parallel simulators developed in this study, which can be the only realistic option in these complex simulations of large multi-dimensional domains.

Influence of adenosine on cerebral blood flow during hypoxic hypoxia in the newborn piglet

1990 ◽  
Vol 68 (4) ◽  
pp. 1534-1541 ◽  
Author(s):  
N. Laudignon ◽  
E. Farri ◽  
K. Beharry ◽  
J. Rex ◽  
J. V. Aranda
Keyword(s):  
Blood Flow ◽  
Cerebral Blood Flow ◽  
High Performance ◽  
Severe Hypoxia ◽  
Group 4 ◽  
Csf Levels ◽  
Group 3 ◽  
Group 2 ◽  
Arterial Po2 ◽  
Group 1

This study investigated the role of adenosine in the regulation of neonatal cerebral blood flow (CBF) during moderate (arterial PO2 = 47 +/- 9 Torr) and severe (arterial PO2 = 25 +/- 4 Torr) hypoxia. Twenty-eight anesthetized and ventilated newborn piglets were assigned to four groups: 8 were injected intravenously with the vehicle (controls, group 1); 13 received an intravenous injection of 8-phenyltheophylline (8-PT), a potent adenosine receptor blocker, either 4 mg/kg (group 2, n = 6, mean cerebrospinal fluid (CSF) levels less than 1 mg/l) or 8 mg/kg (group 3, n = 7, mean CSF levels less than 3.5 mg/l); and 7 received an intracerebroventricular injection of 10 micrograms 8-PT (group 4). During normoxia, CBF was not altered by vehicle or 8-PT injections. In group 1, 10 min of moderate and severe hypoxia increased total CBF by 112 +/- 36 and 176 +/- 28% (SE), respectively. Compared with controls, the cerebral hyperemia during moderate hypoxia was not altered in group 2, attenuated in group 3 (to 53 +/- 13%, P = NS), and completely blocked in group 4 (P less than 0.01). CBF increase secondary to severe hypoxia was attenuated only in group 4 (74 +/- 29%, P less than 0.05). CSF concentrations of adenosine and adenosine metabolites measured by high-performance liquid chromatography increased during hypoxia. Arterial O2 content was inversely correlated (P less than 0.005) to maximal CSF levels of adenosine (r = 0.73), inosine (r = 0.87), and hypoxanthine (r = 0.80).(ABSTRACT TRUNCATED AT 250 WORDS)

Cyclosporine Dose, Serum Trough Levels, and Allograft Preservation in a Rat Model of Laryngeal Transplantation

2003 ◽  
Vol 112 (6) ◽  
pp. 506-510 ◽  
Author(s):  
Marcus Haug ◽  
Michael Fritz ◽  
Olivia Dan ◽  
Robert R. Lorenz ◽  
Sophie Wimberley ◽  
...  
Keyword(s):  
Rat Model ◽  
High Performance ◽  
Group 4 ◽  
Serum Trough ◽  
Group 3 ◽  
The Mean ◽  
Group 5 ◽  
Group 2 ◽  
Trough Levels ◽  
Group 1

Using a rat model of laryngeal transplantation, we sought to define the relationships between acute laryngeal rejection grade (RG) and cyclosporin A (CSA) concentration and CSA dosage. Five recipient Lewis rat groups (N = 10 per group) were administered intramuscular CSA doses of 1.0 (group 1), 2.5 (group 2), 5.0 (group 3), 7.5 (group 4), and 10 mg/kg per day (group 5) for 14 days. Immediately before sacrifice, 5 mL of whole blood was obtained to assay CSA trough levels by high-performance liquid chromatography. The specimens were graded microscopically by blinded reviewers by day of RG, 0 to 14 days after transplantation, as described in earlier reports. Despite high intragroup variability in CSA levels, significantly different mean CSA concentrations were achieved among all CSA dosage groups: 1,2,3,4, and 5 (.0001 < p < .02). The mean laryngeal RGs did not test significantly different from each other with groups 3, 4, and 5 (RG, 2.3 ± 1.3 versus 1.9 ± 1.1 versus 1.7 ±0.3, respectively, .2 < p < .6). The RG for group 1 was significantly greater than those for groups 2 through 5 (p < .001), and the group 2 RG was greater (p < .02) than those for groups 3, 4, and 5. Polynomial fitting was used to determine the continuous relationship between each individual specimen's CSA concentration and the RG. Significant pathological allograft rejection correlated with CSA concentrations below 250 ng/mL.

scholarly journals Migrating Engineering Windows HPC applications to Linux HTCondor and Slurm Clusters

2020 ◽  
Vol 245 ◽  
pp. 09016
Author(s):  
Maria Alandes Pradillo ◽  
Nils Høimyr ◽  
Pablo Llopis Sanmillan ◽  
Markus Tapani Jylhänkangas
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Technology Development ◽  
General Purpose ◽  
Low Latency ◽  
Technical Solution ◽  
Single Node ◽  
It Department ◽  
Linux Cluster

The CERN IT department has been maintaining different High Performance Computing (HPC) services over the past five years. While the bulk of computing facilities at CERN are running under Linux, a Windows cluster was dedicated for engineering simulations and analysis related to accelerator technology development. The Windows cluster consisted of machines with powerful CPUs, big memory, and a low-latency interconnect. The Linux cluster resources are accessible through HTCondor, and are used for general purpose parallel but single-node type jobs, providing computing power to the CERN experiments and departments for tasks such as physics event reconstruction, data analysis, and simulation. For HPC workloads that require multi-node parallel environments for Message Passing Interface (MPI) based programs, there is another Linux-based HPC service that is comprised of several clusters running under the Slurm batch system, and consist of powerful hardware with low-latency interconnects. In 2018, it was decided to consolidate compute intensive jobs in Linux to make a better use of the existing resources. Moreover, this was also in line with CERN IT strategy to reduce its dependencies on Microsoft products. This paper focuses on the migration of Ansys [1], COMSOL [2] and CST [3] users from Windows HPC to Linux clusters. Ansys, COMSOL and CST are three engineering applications used at CERN for different domains, like multiphysics simulations and electromagnetic field problems. Users of these applications are in different departments, with different needs and levels of expertise. In most cases, the users have no prior knowledge of Linux. The paper will present the technical strategy to allow the engineering users to submit their simulations to the appropriate Linux cluster, depending on their simulation requirements. We also describe the technical solution to integrate their Windows workstations in order from them to be able to submit to Linux clusters. Finally, we discuss the challenges and lessons learnt during the migration.

scholarly journals Effect of hemoglobin F and A2 on hemoglobin A1c determined by cation exchange high-performance liquid chromatography

2019 ◽  
Vol 43 (5) ◽  
pp. 265-268
Author(s):  
Murat Can ◽  
Berrak Güven ◽  
Ayse Semra Demir Akca
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
Hemoglobin A1c ◽  
Potential Effect ◽  
Hplc Method ◽  
Hemoglobin F ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

Abstract Background The potential effect of increase in hemoglobin (Hb) A2 and HbF on glycated hemoglobin (HbA1c) measurements were investigated using a high-performance liquid chromatography (HPLC) method compared with an immunoturbimetric assay. Methods Samples producing abnormal chromatograms during the measurement of routine HbA1c testing with HPLC were further analyzed to characterize abnormal Hb variants. Patients were divided into three groups that had only high HbF (group 1), only high HbA2 (group 2), and both high HbA2 and HbF (group 3). HbA1c values of patients were re-assayed using the immunoturbidimetric method (Advia, Siemens Healthcare, Germany). Results HbA1c levels were significantly higher in all groups measured by immunoassay than in HPLC. We found a positive correlation between HPLC and immunoturbidimetry in the group 2 and a slight correlation in the group 1. There was no correlation between the two methods in group 3. Conclusions HbA1c measurement by HPLC method interfering with elevated HbA2 and HbF, especially HbF, should be verified by an immunoturbidimetric method.

The Penetration of Ofloxacin into Human Aqueous Humor Given by Various Routes

1998 ◽  
Vol 8 (1) ◽  
pp. 33-36 ◽  
Author(s):  
S. Hanioglu-Kargi ◽  
N. Basci ◽  
H. Soysal ◽  
A. Bozkurt ◽  
E. Gürsel ◽  
...  
Keyword(s):  
Aqueous Humor ◽  
Bacterial Infections ◽  
High Performance ◽  
Cataract Extraction ◽  
The Other ◽  
Group 4 ◽  
Significant Difference ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

This study was designed to measure the concentration of ofloxacin in aqueous humor after topical, oral and intravenous administration in 50 patients undergoing cataract extraction. In Group 1, ofloxacin 0.3% eyedrops were topically instilled ten times and the aqueous humor concentration was 2.73 ± 0.88 μg/ml. In Group 2, ofloxacin 0.3% eyedrops were topically instilled six times and the aqueous humor concentration was 0.84 ± 0.61 μg/ml. Aqueous humor concentration 12 hours after 200 mg oral dose in Group 3, was 0.38 ± 0.12 μg/ml. In Group 4, patients were given ofloxacin as a single intravenous 200 mg dose and the aqueous humor concentration 2 hours after the end of infusion was 0.45 ± 0.11 μg/ml. Concentrations were determined by high performance liquid chromatography (HPLC) with fluorescence detection. There was a significant difference between Group 1 and the other groups, but not between Group 2 and Groups 3, 4. It was concluded that ofloxacin penetrates the corneal and the blood-aqueous barriers and can achieve good aqueous levels when given topically and systematically. Ofloxacin can be applied topically for external bacterial infections such as conjunctivitis and keratitis. Systematically administered ofloxacin reached higher levels than the MIC for some bacteria which cause endophthalmitis.

In-vivo evaluation of the effect of cyanoacrylate on prosthetic vascular graft infection – does cyanoacrylate increase the severity of infection?

VASA ◽  
2020 ◽  
Vol 49 (4) ◽  
pp. 281-284
Author(s):  
Atıf Yolgosteren ◽  
Gencehan Kumtepe ◽  
Melda Payaslioglu ◽  
Cuneyt Ozakin
Keyword(s):  
Vascular Graft ◽  
Graft Infection ◽  
Vascular Graft Infection ◽  
Group 4 ◽  
Significant Difference ◽  
Group 3 ◽  
Group 2 ◽  
Prosthetic Vascular Graft Infection ◽  
Group 1

Summary. Background: Prosthetic vascular graft infection (PVGI) is a complication with high mortality. Cyanoacrylate (CA) is an adhesive which has been used in a number of surgical procedures. In this in-vivo study, we aimed to evaluate the relationship between PVGI and CA. Materials and methods: Thirty-two rats were equally divided into four groups. Pouch was formed on back of rats until deep fascia. In group 1, vascular graft with polyethyleneterephthalate (PET) was placed into pouch. In group 2, MRSA strain with a density of 1 ml 0.5 MacFarland was injected into pouch. In group 3, 1 cm 2 vascular graft with PET piece was placed into pouch and MRSA strain with a density of 1 ml 0.5 MacFarland was injected. In group 4, 1 cm 2 vascular graft with PET piece impregnated with N-butyl cyanoacrylate-based adhesive was placed and MRSA strain with a density of 1 ml 0.5 MacFarland was injected. All rats were scarified in 96th hour, culture samples were taken where intervention was performed and were evaluated microbiologically. Bacteria reproducing in each group were numerically evaluated based on colony-forming unit (CFU/ml) and compared by taking their average. Results: MRSA reproduction of 0 CFU/ml in group 1, of 1410 CFU/ml in group 2, of 180 200 CFU/ml in group 3 and of 625 300 CFU/ml in group 4 was present. A statistically significant difference was present between group 1 and group 4 (p < 0.01), between group 2 and group 4 (p < 0.01), between group 3 and group 4 (p < 0.05). In terms of reproduction, no statistically significant difference was found in group 1, group 2, group 3 in themselves. Conclusions: We observed that the rate of infection increased in the cyanoacyrylate group where cyanoacrylate was used. We think that surgeon should be more careful in using CA in vascular surgery.

Abnormal Haemostasis and Blood Viscosity in Malignant Hypertension

1984 ◽  
Vol 52 (03) ◽  
pp. 253-255 ◽  
Author(s):  
C Isles ◽  
G D O Lowe ◽  
B M Rankin ◽  
C D Forbes ◽  
N Lucie ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Blood Viscosity ◽  
Renal Damage ◽  
Antithrombin Iii ◽  
Plasma Viscosity ◽  
Malignant Hypertension ◽  
Fibrin Deposition ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

SummaryWe have previously shown abnormalities of haemostasis suggestive of intravascular coagulation in patients with malignant hypertension, a condition associated with retinopathy and renal fibrin deposition. To determine whether such abnormalities are specific to malignant hypertension, we have measured several haemostatic and haemorheological variables in 18 patients with malignant hypertension (Group 1), 18 matched healthy controls (Group 2), and 18 patients with non-malignant hypertension (Group 3) matched for renal pathology, blood pressure and serum creatinine with Group 1. Both Groups 1 and 3 had increased mean levels of fibrinogen, factor VIIIc, beta-thrombo- globulin, plasma viscosity and blood viscosity (corrected for haematocrit); and decreased mean levels of haematocrit, antithrombin III and platelet count. Mean levels of fast antiplasmin and alpha2-macroglobulin were elevated in Group 1 but not in Group 3. We conclude that most blood abnormalities are not specific to malignant hypertension; are also present in patients with non-malignant hypertension who have similar levels of blood pressure and renal damage; and might result from renal damage as well as promoting further renal damage by enhancing fibrin deposition. However increased levels of fibrinolytic inhibitors in malignant hypertension merit further investigation in relation to removal of renal fibrin.

Features of postoperative period in patients with chronic venous insufficiency: phlebectomy versus thermal ablation

2020 ◽  
pp. 64-75
Author(s):  
E. Burleva ◽  
O. Smirnov ◽  
S. Tyurin
Keyword(s):  
Postoperative Period ◽  
Chronic Venous Insufficiency ◽  
Thermal Ablation ◽  
Venous Insufficiency ◽  
Clinical Symptoms ◽  
Varicose Veins ◽  
Statistical Processing ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

The purpose of the study was to conduct a comparative assessment of the course of the postoperative period after phlebectomy and thermal ablation in patients with varicose veins of the lower extremities in the system of the great saphenous vein (GSV) with class C2 of chronic venous insufficiency (CVI) — CEAP class C2. Materials and methods: 455 patients (455 limbs) with CEAP class C2. Group 1 (n = 154) received stripping + minimally invasive phlebectomy; Group 2 — endovenous laser ablation (EVLA) of GSV trunk + sclerotherapy of varicose veins; 3 group (n = 150) — radiofrequency ablation (RFA) of the GSV + sclerotherapy. All patients were united by a single tactical solution — the elimination of pathological vertical reflux in GSV. In each group, patients were with similar hemodynamic profile were selected (Group 1 = 63; Group 2 = 61; Group 3 = 61). The course of the postoperative period (from 2 days to 2 months) was compared for pain (visual analog scale — VAS), clinical symptoms of chronic venous insufficiency, degree of satisfaction (Darvall questionnaire), and duration of disability. Statistical processing was carried out using Excel programs for Windows XP, MedCalc® (version 11.4.2.0., Mariakerke, Belgium). Results: Postoperative pain is more pronounced (during day 1 for Group 1–4.0, Group 2–3.0, Group 3–2.0) and more prolonged (up to 4 days) after open surgeries (p < 0.05). The dynamics of the clinical symptoms of CVI (including varicose syndrome and use of compression therapy) could not be fully evaluated in connection with the ongoing sclerotherapy procedures for patients of Groups 2 and 3. Satisfaction of patients with aesthetic aspects was higher than expected in all groups. Reliable statistical differences proved decrease in days of disability (Group 1–14; Group 2–4; Group 3–3) and earlier return to physical activities and work in patients after thermal ablation in comparison with phlebectomy. Conclusion: The study shows that all three methods for eliminating vertical reflux in the GSV can be proposed for a large category of patients with CEAP of class C3 and C2. Medical and social rehabilitation of patients using endovascular thermal ablation technologies proceeds faster, which is beneficial both for the patients and for society.

Analysis of the quality of early diagnostics of cardiovascular diseases in students of educational institutions of Khabarovsk (according to the data of preventive examinations)

2020 ◽  
pp. 13-16
Keyword(s):  
Blood Pressure ◽  
Cardiovascular Diseases ◽  
Sinus Tachycardia ◽  
Blood Pressure Level ◽  
Educational Institutions ◽  
Conduction Disturbances ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

To identify the prevalence of early pathology of cardiovascular diseases, a survey of 400 200 girls) in the age group 15 and 17 years old was conducted as a part of routine medical of the level of blood pressure (BP) was carried out, with the calculation of the average level pressure on the basis of three separate measurements estimated by percentile tables for a registration of a standard resting ECG in 12 leads. According to the results of the survey, into 3 groups: with an increase in blood pressure above 95 ‰ (group 1 – 16 people), which recorded in males (p<0,05); Group 2 (67 people) – adolescents with a normal blood pressure level and group 3 of adolescents with a decrease in blood pressure below 5 ‰ changes in the form of rhythm and conduction disturbances were noted in almost every a predominance of sinus tachycardia in the first group. In the third group of adolescents, form of ectopic rhythm and pacemaker migration were significantly more frequently only 78 % of adolescents were referred for consultation and in-depth examination by a pediatric cardiologist.

Does Perioperative Hemoglobin A1c Level Affect the Incidence, Pattern and Mortality of Lower Extremity Amputation?

2019 ◽  
Vol 17 (4) ◽  
pp. 354-364
Author(s):  
Hassan Al-Thani ◽  
Moamena El-Matbouly ◽  
Maryam Al-Sulaiti ◽  
Noora Al-Thani ◽  
Mohammad Asim ◽  
...  
Keyword(s):  
Glycemic Control ◽  
Lower Extremity ◽  
Hazard Ratio ◽  
Lower Extremity Amputation ◽  
Group 4 ◽  
Group 3 ◽  
Group 5 ◽  
Group 2 ◽  
Extremity Amputation ◽  
Group 1

Background: We hypothesized that perioperative HbA1c influenced the pattern and outcomes of Lower Extremity Amputation (LEA). Methods: A retrospective analysis was conducted for all patients who underwent LEA between 2000 and 2013. Patients were categorized into 5 groups according to their perioperative HbA1c values [Group 1 (<6.5%), Group 2 (6.5-7.4%), Group 3 (7.5-8.4%), Group 4 (8.5-9.4%) and Group 5 (≥9.5%)]. We identified 848 patients with LEA; perioperative HbA1c levels were available in 547 cases (Group 1: 18.8%, Group 2: 17.7%, Group 3: 15.0%, Group 4: 13.5% and Group 5: 34.9%). Major amputation was performed in 35%, 32%, 22%, 10.8% and 13.6%, respectively. Results: The overall mortality was 36.5%; of that one quarter occurred during the index hospitalization. Mortality was higher in Group 1 (57.4%) compared with Groups 2-5 (46.9%, 38.3%, 36.1% and 31.2%, respectively, p=0.001). Cox regression analysis showed that poor glycemic control (Group 4 and 5) had lower risk of mortality post-LEA [hazard ratio 0.57 (95% CI 0.35-0.93) and hazard ratio 0.46 (95% CI 0.31-0.69)]; this mortality risk persisted even after adjustment for age and sex but was statistically insignificant. The rate of LEA was greater among poor glycemic control patients; however, the mortality was higher among patients with tight control. Conclusion: The effects of HbA1c on the immediate and long-term LEA outcomes and its therapeutic implications need further investigation.

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